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Found 1 Document (0.823 seconds)

BMRB: 15555

2JXD

NMR structure of human Serine protease inhibitor Kazal type II (SPINK2)

Authors

Ting, C., Tian-Ren, L., Ping-Chiang, L.

Assembly

SPINK2 monomer

Entity

1. SPINK2 monomer (polymer, Thiol state: all disulfide bound), 62 monomers, 7009.047 Da Detail

PQFGLFSKYR TPNCSQYRLP GCPRHFNPVC GSDMSTYANE CTLCMKIREG GHNIKIIRNG PC

Formula weight

7009.047 Da

Entity Connection

disulfide 3 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS14:SG	1:CYS44:SG
2	disulfide	sing	1:CYS22:SG	1:CYS41:SG
3	disulfide	sing	1:CYS30:SG	1:CYS62:SG

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing, Water refinement

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.8 %, Completeness: 81.2 %, Completeness (bb): 96.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H
All	81.2 % (311 of 383)	81.2 % (311 of 383)
Backbone	96.8 % (120 of 124)	96.8 % (120 of 124)
Sidechain	73.7 % (191 of 259)	73.7 % (191 of 259)
Aromatic	67.7 % (21 of 31)	67.7 % (21 of 31)
Methyl	75.0 % (15 of 20)	75.0 % (15 of 20)

1. SPINK2

PQFGLFSKYR TPNCSQYRLP GCPRHFNPVC GSDMSTYANE CTLCMKIREG GHNIKIIRNG PC

Show sample condition

Sample

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 3.7, Details in aqueous solution (100% H2O)

#	Name	Isotope labeling	Concentration
1	SPINK2	natural abundance	1.5 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %

Protein Blocks Logo

Calculated from 15 models in PDB: 2JXD, Strand ID: A Detail

Release date

2009-05-17

Citation

Identification of trypsin-inhibitory site and structure determination of human SPINK2 serine proteinase inhibitor
Chen, T., Lee, T., Liang, W., Chang, W., Lyu, P.
Proteins (2009), 77, 209-219, PubMed 19422058 , DOI 10.1002/prot.22432 , Abstract

Entries sharing articles Swiss-Prot: 1 entries Detail

Swiss-Prot: P20155 released on 1991-02-01
Title ISK2_HUMAN Entity Serine protease inhibitor Kazal-type 2

Related entities 1. SPINK2 monomer, : 1 : 2 : 185 entities Detail

Interaction partners 1. SPINK2 monomer, : 3 interactors Detail

More details for 3 interactors identified by 1 citations

Experiments performed 1 experiments Detail

NMR combined restraints 8 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15555_2jxd.nef
Input source #2: Coordindates	2jxd.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	None
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 (Å)
A:14:CYS:SG	A:44:CYS:SG	unknown	unknown	2.016
A:22:CYS:SG	A:41:CYS:SG	unknown	unknown	2.014
A:30:CYS:SG	A:62:CYS:SG	unknown	unknown	2.015

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--
PQFGLFSKYRTPNCSQYRLPGCPRHFNPVCGSDMSTYANECTLCMKIREGGHNIKIIRNGPC
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
PQFGLFSKYRTPNCSQYRLPGCPRHFNPVCGSDMSTYANECTLCMKIREGGHNIKIIRNGPC

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	62	0	0	100.0

Content subtype: combined_15555_2jxd.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	3		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	317		96.8 (chain: A, length: 62)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	224 (1)	noe	64.5 (chain: A, length: 62)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	974 (1)	noe	96.8 (chain: A, length: 62)
3	Distance restraints	CNS/XPLOR_distance_constraints_8	Warning	3 (1)	undefined	9.7 (chain: A, length: 62)
4	Distance restraints	CNS/XPLOR_distance_constraints_6	OK	96 (1)	noe	54.8 (chain: A, length: 62)
5	Distance restraints	CNS/XPLOR_distance_constraints_7	Warning	20 (1)	hbond	27.4 (chain: A, length: 62)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_9	OK	32 (32)	.	53.2 (chain: A, length: 62)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 62, Sequence coverage: 96.8%
- Total number of assignments
  - ¹H chemical shifts: 317
- Completeness of assignments
  - Entity_assemble_ID: A
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
10	ARG	HH11	7.007

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	383	314	82.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	124	122	98.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	259	192	74.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	22	15	68.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	31	21	67.7

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 62, Sequence coverage: 64.5%
- Total number of restraints: 214
- Weight of restraints: 1.0 (214)
- Potential type of restraints: square-well-parabolic (214)
- Range of distance target values: 2.15, 4.5 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 62, Sequence coverage: 96.8%
  - Total number of restraints: 946
  - Weight of restraints: 1.0 (946)
  - Potential type of restraints: square-well-parabolic (946)
  - Range of distance target values: 2.65, 4.5 (Å)
  - Histogram of distance target values
  - Histogram of discrepancy in distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_8
    - Status: Warning
    - Experiment type: undefined
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 62, Sequence coverage: 9.7%
    - Total number of restraints: 3
    - Weight of restraints: 1.0 (3)
    - Potential type of restraints: square-well-parabolic (3)
    - Range of distance target values: 2.0, 2.0 (Å)
    - Distance restraints per residue
      - Chain_ID: A
    - Distance restraints on contact map
    - Saveframe: CNS/XPLOR_distance_constraints_6
      - Status: OK
      - Experiment type: noe
      - Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 62, Sequence coverage: 54.8%
        --------10--------20--------30--------40--------50--------60-- PQFGLFSKYRTPNCSQYRLPGCPRHFNPVCGSDMSTYANECTLCMKIREGGHNIKIIRNGPC || |||| |||||| ||| || ||||||||||||| | | | | .QF....KYRT.NCSQYR.......FNP.CG......ANECTLCMKIREG..N.K.I....C
      - Total number of restraints: 94
        Intra-residue restraints, i = j : 36
        Sequential restraints, | i - j | = 1 : 12
        Backbone-backbone: 4
        Backbone-side chain: 6
        Side chain-side chain: 2
        Medium range restraints, 1 < | i - j | < 5 : 24
        Backbone-backbone: 5
        Backbone-side chain: 7
        Side chain-side chain: 12
        Long range restraints, | i - j | >= 5 : 22
      - Weight of restraints: 1.0 (94)
        Intra-residue restraints, i = j : 1.0 (36)
        Sequential restraints, | i - j | = 1 : 1.0 (12)
        Backbone-backbone: 1.0 (4)
        Backbone-side chain: 1.0 (6)
        Side chain-side chain: 1.0 (2)
        Medium range restraints, 1 < | i - j | < 5 : 1.0 (24)
        Backbone-backbone: 1.0 (5)
        Backbone-side chain: 1.0 (7)
        Side chain-side chain: 1.0 (12)
        Long range restraints, | i - j | >= 5 : 1.0 (22)
      - Potential type of restraints: square-well-parabolic (94)
        Intra-residue restraints, i = j : square-well-parabolic (36)
        Sequential restraints, | i - j | = 1 : square-well-parabolic (12)
        Backbone-backbone: square-well-parabolic (4)
        Backbone-side chain: square-well-parabolic (6)
        Side chain-side chain: square-well-parabolic (2)
        Medium range restraints, 1 < | i - j | < 5 : square-well-parabolic (24)
        Backbone-backbone: square-well-parabolic (5)
        Backbone-side chain: square-well-parabolic (7)
        Side chain-side chain: square-well-parabolic (12)
        Long range restraints, | i - j | >= 5 : square-well-parabolic (22)
      - Range of distance target values: 3.0, 4.5 (Å)
      - Histogram of distance target values
      - Distance restraints per residue
        Chain_ID: A
      - Distance restraints on contact map
        Chain_ID_1: A - Chain_ID_2: A
      - Saveframe: CNS/XPLOR_distance_constraints_7
        Status: Warning
        Experiment type: hbond
        Sequence coverage of experimental data
        Entity_assembly_ID: A, Chain length: 62, Sequence coverage: 27.4%
        Total number of restraints: 20
        Total hydrogen bond restraints: 20
        O...h-N: 6
        O...H-x: 6
        Long range: 8
        O...h-N: 4
        O...H-x: 4
        Weight of restraints: 1.0 (20)
        Total hydrogen bond restraints: 1.0 (20)
        O...h-N: 1.0 (6)
        O...H-x: 1.0 (6)
        Long range: 1.0 (8)
        O...h-N: 1.0 (4)
        O...H-x: 1.0 (4)
        Potential type of restraints: square-well-parabolic (20)
        Total hydrogen bond restraints: square-well-parabolic (20)
        O...h-N: square-well-parabolic (6)
        O...H-x: square-well-parabolic (6)
        Long range: square-well-parabolic (8)
        O...h-N: square-well-parabolic (4)
        O...H-x: square-well-parabolic (4)
        Range of distance target values: 2.0, 2.9 (Å)
        Histogram of distance target values
        Distance restraints per residue
        Chain_ID: A
        Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_9
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 62, Sequence coverage: 53.2%
- Total number of restraints: 32
- Total number of restraints per polymer type: 32
- Weight of restraints: 1.0 (32)
- Potential type of restraints: square-well-parabolic (32)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords alpha helix, anti-parallel beta sheet, beta-bulge, disulfide bond

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Found 1 Document (0.823 seconds)

BMRB: 15555

Sample

Entries sharing articles Swiss-Prot: 1 entries Detail

Related entities 1. SPINK2 monomer, : 1 : 2 : 185 entities Detail

Interaction partners 1. SPINK2 monomer, : 3 interactors Detail

Experiments performed 1 experiments Detail

Instrument

Sample

NMR combined restraints 8 contents Detail