Properties
Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints | combined_15637_2k05.nef |
Input source #2: Coordindates | 2k05.cif |
Diamagnetism of the molecular assembly | True (excluding Oxygen atoms) |
Whether the assembly has a disulfide bond | True (see coordinates for details) |
Whether the assembly has a other bond | True (see coodinates for details) |
Whether the assembly contains a cyclic polymer | None |
Overall data processing status | Warning |
Disulfide bonds
Ptnr_site_1 | Ptnr_site_2 | Redox_state_prediction_1 | Redox_state_prediction_2 | Distance (Ã…) |
---|
A:9:CYS:SG | A:34:CYS:SG | oxidized, CA 53.192, CB 40.897 ppm | oxidized, CA 55.447, CB 45.228 ppm | 2.03 |
A:11:CYS:SG | A:50:CYS:SG | unknown | oxidized, CA 58.054, CB 43.162 ppm | 2.018 |
A:36:CYS:SG | C:265:CYS:SG | oxidized, CA 58.616, CB 45.705 ppm | unknown | 2.046 |
A:65:CYS:SG | C:236:CYS:SG | oxidized, CA 56.329, CB 45.235 ppm | unknown | 2.041 |
C:209:CYS:SG | C:234:CYS:SG | unknown | unknown | 2.01 |
C:211:CYS:SG | C:250:CYS:SG | unknown | unknown | 2.022 |
Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)
Ptnr_site_1 | Ptnr_site_2 | Redox_state_prediction_1 | Redox_state_prediction_2 | Distance (Ã…) |
---|
3:8:ILE:C | 3:9:TYS:N | unknown | unknown | n/a |
3:9:TYS:C | 3:10:THR:N | unknown | unknown | n/a |
3:13:ASN:C | 3:14:TYS:N | unknown | unknown | n/a |
3:14:TYS:C | 3:15:THR:N | unknown | unknown | n/a |
3:22:ASP:C | 3:23:TYS:N | unknown | unknown | n/a |
3:23:TYS:C | 3:24:ASP:N | unknown | unknown | n/a |
4:8:ILE:C | 4:9:TYS:N | unknown | unknown | n/a |
4:9:TYS:C | 4:10:THR:N | unknown | unknown | n/a |
4:13:ASN:C | 4:14:TYS:N | unknown | unknown | n/a |
4:14:TYS:C | 4:15:THR:N | unknown | unknown | n/a |
4:22:ASP:C | 4:23:TYS:N | unknown | unknown | n/a |
4:23:TYS:C | 4:24:ASP:N | unknown | unknown | n/a |
Non-standard residues
Chain_ID | Seq_ID | Comp_ID | Chem_comp_name | Experimental evidences |
---|
B | 107 | TYS | O-SULFO-L-TYROSINE | Assigned chemical shifts, Distance restraints, Coordinates |
B | 112 | TYS | O-SULFO-L-TYROSINE | Assigned chemical shifts, Distance restraints, Coordinates |
B | 121 | TYS | O-SULFO-L-TYROSINE | Assigned chemical shifts, Distance restraints, Coordinates |
D | 307 | TYS | O-SULFO-L-TYROSINE | Distance restraints, Coordinates |
D | 312 | TYS | O-SULFO-L-TYROSINE | Distance restraints, Coordinates |
D | 321 | TYS | O-SULFO-L-TYROSINE | Distance restraints, Coordinates |
Sequence alignments
- Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A
-0--------10--------20--------30--------40--------50--------60--------
GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCACQIVARLKNNNRQVCIDPKLKWIQEYLEKCLNK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCACQIVARLKNNNRQVCIDPKLKWIQEYLEKCLNK
--------10--------20--------30--------40--------50--------60--------70
Entity_assembly_ID (NMR): B vs Auth_asym_ID (model): B-100-----110-------120-------130--------
GSMEGISIXTSDNXTEEMGSGDXDSMKEPAFREENANFNK
||||||||||||||||||||||||||||||||||||||||
GSMEGISIXTSDNXTEEMGSGDXDSMKEPAFREENANFNK
--------10--------20--------30--------40
Entity_assembly_ID (NMR): C vs Auth_asym_ID (model): C-200-----210-------220-------230-------240-------250-------260--------
GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCACQIVARLKNNNRQVCIDPKLKWIQEYLEKCLNK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCACQIVARLKNNNRQVCIDPKLKWIQEYLEKCLNK
--------10--------20--------30--------40--------50--------60--------70
Entity_assembly_ID (NMR): D vs Auth_asym_ID (model): D-300-----310-------320-------330--------
GSMEGISIXTSDNXTEEMGSGDXDSMKEPAFREENANFNK
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GSMEGISIXTSDNXTEEMGSGDXDSMKEPAFREENANFNK
--------10--------20--------30--------40
Chain assignments
Entity_assembly_ID (NMR) | Auth_asym_ID (model) | Length | Unmapped | Conflict | Sequence coverage (%) |
---|
A | A | 70 | 0 | 0 | 100.0 |
B | B | 40 | 0 | 0 | 100.0 |
C | C | 70 | 0 | 0 | 100.0 |
D | D | 40 | 0 | 0 | 100.0 |
Content subtype: combined_15637_2k05.nef
# | Content subtype | Saveframe | Status | # of rows (sets) | Experiment type | Sequence coverage (%) |
---|
1 | Covalent bonds | assembly | OK | 18 | | No information |
1 | Assigned chemical shifts | assigned_chem_shift_list_1 | Warning | 1159 | | 94.3 (chain: A, length: 70), 95.0 (chain: B, length: 40) |
1 | Distance restraints | DYANA/DIANA_distance_constraints_3 | Warning | 2944 (1) | undefined | 88.6 (chain: A, length: 70), 77.5 (chain: B, length: 40), 88.6 (chain: C, length: 70), 77.5 (chain: D, length: 40) |
1 | Dihedral angle restraints | DYANA/DIANA_dihedral_2 | OK | 128 (128) | . | 71.4 (chain: A, length: 70), 71.4 (chain: C, length: 70) |
Assigned chemical shifts
- Saveframe: assigned_chem_shift_list_1
-100-----110-------120-------130--------
GSMEGISIXTSDNXTEEMGSGDXDSMKEPAFREENANFNK
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..MEGISIXTSDNXTEEMGSGDXDSMKEPAFREENANFNK
- Total number of assignments
- 1H chemical shifts: 622
- 13C chemical shifts: 431
- 15N chemical shifts: 106
- Completeness of assignments
- Entity_assemble_ID: A
- All atoms
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|
1H chemical shifts | 461 | 417 | 90.5 |
13C chemical shifts | 330 | 290 | 87.9 |
15N chemical shifts | 82 | 70 | 85.4 |
- Backbone atoms
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|
1H chemical shifts | 137 | 125 | 91.2 |
13C chemical shifts | 140 | 123 | 87.9 |
15N chemical shifts | 66 | 61 | 92.4 |
- Side chain atoms
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|
1H chemical shifts | 324 | 292 | 90.1 |
13C chemical shifts | 190 | 167 | 87.9 |
15N chemical shifts | 16 | 9 | 56.2 |
- Methyl group atoms
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|
1H chemical shifts | 38 | 36 | 94.7 |
13C chemical shifts | 38 | 34 | 89.5 |
- Aromatic group atoms
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|
1H chemical shifts | 28 | 26 | 92.9 |
13C chemical shifts | 27 | 17 | 63.0 |
15N chemical shifts | 1 | 1 | 100.0 |
- Entity_assemble_ID: B
- All atoms
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|
1H chemical shifts | 231 | 205 | 88.7 |
13C chemical shifts | 162 | 141 | 87.0 |
15N chemical shifts | 44 | 36 | 81.8 |
- Backbone atoms
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|
1H chemical shifts | 83 | 76 | 91.6 |
13C chemical shifts | 80 | 73 | 91.2 |
15N chemical shifts | 39 | 36 | 92.3 |
- Side chain atoms
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|
1H chemical shifts | 148 | 129 | 87.2 |
13C chemical shifts | 82 | 68 | 82.9 |
15N chemical shifts | 5 | 0 | 0.0 |
- Methyl group atoms
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|
1H chemical shifts | 11 | 8 | 72.7 |
13C chemical shifts | 11 | 8 | 72.7 |
- Aromatic group atoms
Atom group | # of target shifts | # of assigned shifts | Completeness (%) |
---|
1H chemical shifts | 22 | 21 | 95.5 |
13C chemical shifts | 16 | 11 | 68.8 |
- Redox state of CYS
- A:9:CYS, CA: 53.192 ppm, CB: 40.897 ppm
- Redox_state (pred. by CS): oxidized
- Disulfide_bond (coordinates): True, Other_bond (coordinates): False
- A:34:CYS, CA: 55.447 ppm, CB: 45.228 ppm
- Redox_state (pred. by CS): oxidized
- Disulfide_bond (coordinates): True, Other_bond (coordinates): False
- A:36:CYS, CA: 58.616 ppm, CB: 45.705 ppm
- Redox_state (pred. by CS): oxidized
- Disulfide_bond (coordinates): True, Other_bond (coordinates): False
- A:50:CYS, CA: 58.054 ppm, CB: 43.162 ppm
- Redox_state (pred. by CS): oxidized
- Disulfide_bond (coordinates): True, Other_bond (coordinates): False
- A:65:CYS, CA: 56.329 ppm, CB: 45.235 ppm
- Redox_state (pred. by CS): oxidized
- Disulfide_bond (coordinates): True, Other_bond (coordinates): False
- Peptide bond of PRO
- A:2:PRO, CB: 32.476 ppm, CG: 27.775 ppm
- Peptide_bond (pred. by CS): trans
- Peptide_bond (coordinates): trans
- A:10:PRO, CB: 32.904 ppm, CG: 27.9 ppm
- Peptide_bond (pred. by CS): trans
- Peptide_bond (coordinates): trans
- A:32:PRO, CB: 32.484 ppm, CG: 27.631 ppm
- Peptide_bond (pred. by CS): trans
- Peptide_bond (coordinates): trans
- A:53:PRO, CB: 33.002 ppm, CG: 27.631 ppm
- Peptide_bond (pred. by CS): trans
- Peptide_bond (coordinates): trans
- B:127:PRO, CB: 32.272 ppm, CG: 27.873 ppm
- Peptide_bond (pred. by CS): trans
- Peptide_bond (coordinates): trans
- Tautomeric state of HIS
- A:17:HIS, CG: None ppm, CD2: 120.4 ppm, ND1: None ppm, ND2: None ppm
- Tautomeric_state (pred. by CS): biprotonated 84.4%, tau-tautomer 13.2%, pi-tautomer 2.5%
- Tautomeric_state (coordinates): biprotonated
- A:25:HIS, CG: None ppm, CD2: 123.763 ppm, ND1: None ppm, ND2: None ppm
- Tautomeric_state (pred. by CS): biprotonated 10.9%, tau-tautomer 0.6%, pi-tautomer 88.5%
- Tautomeric_state (coordinates): biprotonated
- Rotameric state of ILE , LEU, and VAL
- A:3:VAL, CG1: 21.324 ppm, CG2: None ppm
- Rotameric_state (pred. by CS): gauche+ 34.2%, trans 34.5%, gauche- 31.3%
- Rotameric_state (coordinates): gauche+
- A:5:LEU, CD1: 25.588 ppm, CD2: None ppm
- Rotameric_state (pred. by CS): gauche+ 44.4%, trans 55.6%, gauche- 0.0%
- Rotameric_state (coordinates): trans
- A:18:VAL, CG1: 22.445 ppm, CG2: None ppm
- Rotameric_state (pred. by CS): gauche+ 21.8%, trans 37.3%, gauche- 40.9%
- Rotameric_state (coordinates): gauche+
- A:23:VAL, CG1: 22.432 ppm, CG2: 21.807 ppm
- Rotameric_state (pred. by CS): gauche+ 25.7%, trans 46.5%, gauche- 27.9%
- Rotameric_state (coordinates): gauche-
- A:26:LEU, CD1: 26.013 ppm, CD2: 24.187 ppm
- Rotameric_state (pred. by CS): gauche+ 31.7%, trans 68.3%, gauche- 0.0%
- Rotameric_state (coordinates): gauche+
- A:28:ILE, CD1: 14.041 ppm
- Rotameric_state (pred. by CS): gauche+ 4.1%, trans 82.1%, gauche- 13.8%
- Rotameric_state (coordinates): trans
- A:29:LEU, CD1: 25.808 ppm, CD2: 23.425 ppm
- Rotameric_state (pred. by CS): gauche+ 26.2%, trans 73.8%, gauche- 0.0%
- Rotameric_state (coordinates): gauche+
- A:38:ILE, CD1: 14.029 ppm
- Rotameric_state (pred. by CS): gauche+ 4.0%, trans 81.9%, gauche- 14.0%
- Rotameric_state (coordinates): trans
- A:39:VAL, CG1: 21.783 ppm, CG2: 21.797 ppm
- Rotameric_state (pred. by CS): gauche+ 32.8%, trans 43.6%, gauche- 23.6%
- Rotameric_state (coordinates): trans
- A:42:LEU, CD1: 26.006 ppm, CD2: 23.452 ppm
- Rotameric_state (pred. by CS): gauche+ 24.5%, trans 75.5%, gauche- 0.0%
- Rotameric_state (coordinates): trans
- A:49:VAL, CG1: 22.121 ppm, CG2: 19.918 ppm
- Rotameric_state (pred. by CS): gauche+ 24.7%, trans 21.6%, gauche- 53.6%
- Rotameric_state (coordinates): gauche-
- A:51:ILE, CD1: 14.665 ppm
- Rotameric_state (pred. by CS): gauche+ 4.6%, trans 93.0%, gauche- 2.5%
- Rotameric_state (coordinates): gauche-
- A:55:LEU, CD1: 26.013 ppm, CD2: 23.425 ppm
- Rotameric_state (pred. by CS): gauche+ 24.1%, trans 75.9%, gauche- 0.0%
- Rotameric_state (coordinates): trans
- A:58:ILE, CD1: 16.953 ppm
- Rotameric_state (pred. by CS): gauche+ 4.7%, trans 95.3%, gauche- 0.0%
- Rotameric_state (coordinates): gauche-
- A:62:LEU, CD1: 26.604 ppm, CD2: 23.313 ppm
- Rotameric_state (pred. by CS): gauche+ 17.1%, trans 82.9%, gauche- 0.0%
- Rotameric_state (coordinates): trans
- A:66:LEU, CD1: 26.013 ppm, CD2: 23.998 ppm
- Rotameric_state (pred. by CS): gauche+ 29.8%, trans 70.2%, gauche- 0.0%
- Rotameric_state (coordinates): gauche-
- B:104:ILE, CD1: 13.418 ppm
- Rotameric_state (pred. by CS): gauche+ 3.5%, trans 71.3%, gauche- 25.1%
- Rotameric_state (coordinates): trans
- B:106:ILE, CD1: 13.418 ppm
- Rotameric_state (pred. by CS): gauche+ 3.5%, trans 71.3%, gauche- 25.1%
- Rotameric_state (coordinates): gauche-
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S2 and NMR RMSD)
Covalent bonds
- Saveframe: assembly
Distance restraints
- Saveframe: DYANA/DIANA_distance_constraints_3
-100-----110-------120-------130--------
GSMEGISIXTSDNXTEEMGSGDXDSMKEPAFREENANFNK
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...EGISIXTSDNXTEEM..GDXDSMKEPAFREE...F.K
- Entity_assembly_ID: C, Chain length: 70, Sequence coverage: 88.6%
-200-----210-------220-------230-------240-------250-------260--------
GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCACQIVARLKNNNRQVCIDPKLKWIQEYLEKCLNK
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....V.LSYRCPCRFFESHVARANVKHLKILNTP.CACQIVARLK..NRQVCIDPKLKWIQEYLEKCLNK
- Entity_assembly_ID: D, Chain length: 40, Sequence coverage: 77.5%
-300-----310-------320-------330--------
GSMEGISIXTSDNXTEEMGSGDXDSMKEPAFREENANFNK
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...EGISIXTSDNXTEEM..GDXDSMKEPAFREE...F.K
- Total number of restraints: 2940
- Intra-residue restraints, i = j : 1198
- Sequential restraints, | i - j | = 1 : 560
- Backbone-backbone: 70
- Backbone-side chain: 398
- Side chain-side chain: 92
- Medium range restraints, 1 < | i - j | < 5 : 322
- Backbone-backbone: 36
- Backbone-side chain: 104
- Side chain-side chain: 182
- Long range restraints, | i - j | >= 5 : 580
- Inter-chain restraints: 14
- Total hydrogen bond restraints: 32
- Total disulfide bond restraints: 6
- Symmetric restraints: 228
- Weight of restraints: 1.0 (2940)
- Intra-residue restraints, i = j : 1.0 (1198)
- Sequential restraints, | i - j | = 1 : 1.0 (560)
- Backbone-backbone: 1.0 (70)
- Backbone-side chain: 1.0 (398)
- Side chain-side chain: 1.0 (92)
- Medium range restraints, 1 < | i - j | < 5 : 1.0 (322)
- Backbone-backbone: 1.0 (36)
- Backbone-side chain: 1.0 (104)
- Side chain-side chain: 1.0 (182)
- Long range restraints, | i - j | >= 5 : 1.0 (580)
- Inter-chain restraints: 1.0 (14)
- Total hydrogen bond restraints: 1.0 (32)
- Total disulfide bond restraints: 1.0 (6)
- Symmetric restraints: 1.0 (228)
- Potential type of restraints: upper-bound-parabolic (2940)
- Intra-residue restraints, i = j : upper-bound-parabolic (1198)
- Sequential restraints, | i - j | = 1 : upper-bound-parabolic (560)
- Backbone-backbone: upper-bound-parabolic (70)
- Backbone-side chain: upper-bound-parabolic (398)
- Side chain-side chain: upper-bound-parabolic (92)
- Medium range restraints, 1 < | i - j | < 5 : upper-bound-parabolic (322)
- Backbone-backbone: upper-bound-parabolic (36)
- Backbone-side chain: upper-bound-parabolic (104)
- Side chain-side chain: upper-bound-parabolic (182)
- Long range restraints, | i - j | >= 5 : upper-bound-parabolic (580)
- Inter-chain restraints: upper-bound-parabolic (14)
- Total hydrogen bond restraints: upper-bound-parabolic (32)
- Total disulfide bond restraints: upper-bound-parabolic (6)
- Symmetric restraints: upper-bound-parabolic (228)
- Range of distance target values: 2.0, 5.5 (Ã…)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
- Chain_ID: A
- Chain_ID: B
- Chain_ID: C
- Chain_ID: D
- Distance restraints on contact map
- Chain_ID_1: A - Chain_ID_2: A
- Chain_ID_1: B - Chain_ID_2: B
- Chain_ID_1: C - Chain_ID_2: C
- Chain_ID_1: D - Chain_ID_2: D
- Chain_ID_1: A - Chain_ID_2: B
- Chain_ID_1: A - Chain_ID_2: C
- Chain_ID_1: A - Chain_ID_2: D
- Chain_ID_1: B - Chain_ID_2: C
- Chain_ID_1: B - Chain_ID_2: D
None
- Chain_ID_1: C - Chain_ID_2: D
Dihedral angle restraints
- Saveframe: DYANA/DIANA_dihedral_2
-200-----210-------220-------230-------240-------250-------260--------
GMKPVSLSYRCPCRFFESHVARANVKHLKILNTPNCACQIVARLKNNNRQVCIDPKLKWIQEYLEKCLNK
|||||||||| |||||||||||||||||| |||||| |||||| ||||||||||
........YRCPCRFFES.VARANVKHLKILNTPNCA.QIVARL....RQVCID...KWIQEYLEKC
-200-----210-------220-------230-------240-------250-------260-----
- Total number of restraints: 128
- Phi angle constraints: 66
- Psi angle constraints: 62
- Total number of restraints per polymer type: 128
- Weight of restraints: 1.0 (128)
- Phi angle constraints: 1.0 (66)
- Psi angle constraints: 1.0 (62)
- Potential type of restraints: square-well-parabolic (128)
- Phi angle constraints: square-well-parabolic (66)
- Psi angle constraints: square-well-parabolic (62)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue