BMRBj - BMREntryMaster

Found 1 Document (0.615 seconds)

BMRB: 30267

5V2G

De Novo Design of Novel Covalent Constrained Meso-size Peptide Scaffolds with Unique Tertiary Structures

Authors

Dang, B., Wu, H., Mulligan, V.K., Mravic, M., Wu, Y., Lemmin, T., Ford, A., Silva, D., Baker, D., DeGrado, W.F.

Assembly

20-mer Peptide

Entity

1. 20-mer Peptide (polymer, Thiol state: not present), 20 monomers, 2263.481 × 3 Da Detail

KNPEAEEITR CKKLLDDSSS

2. 1,3,5-tris(bromomethyl)benzene (non-polymer), 356.880 Da

Total weight

7147.3228 Da

Max. entity weight

2263.481 Da

Source organism

synthetic construct

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 75.0 %, Completeness (bb): 81.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C
All	75.0 % (156 of 208)	78.7 % (96 of 122)	69.8 % (60 of 86)
Backbone	81.8 % (81 of 99)	100.0 % (39 of 39)	70.0 % (42 of 60)
Sidechain	73.6 % (95 of 129)	68.7 % (57 of 83)	82.6 % (38 of 46)
Methyl	93.8 % (15 of 16)	87.5 % (7 of 8)	100.0 % (8 of 8)

1. 20-mer Peptide

KNPEAEEITR CKKLLDDSSS

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 (±0.0) atm, Temperature 285 (±0.5) K, pH 4.0 (±0.1), Details 0.7 mM non-label 1, 95% H2O/5% D2O

#	Name	Isotope labeling	Type	Concentration
1	1	natural abundance		0.7 (±0.05) mM

Protein Blocks Logo

Calculated from 20 models in PDB: 5V2G, Strand ID: A, B, C Detail

Release date

2017-06-19

Citation

De novo design of covalently constrained mesosize protein scaffolds with unique tertiary structures
Dang, B., Wu, H., Mulligan, V.K., Mravic, M., Wu, Y., Lemmin, T., Ford, A., Silva, D.A., Baker, D., DeGrado, W.F.
Proc. Natl. Acad. Sci. U. S. A. (2017), 114, 10852-10857, PubMed 28973862 , DOI 10.1073/pnas.1710695114 , Abstract

Related entities 1. 20-mer Peptide, : 2 entities Detail

Experiments performed 4 experiments Detail

NMR combined restraints 3 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints	combined_30267_5v2g.nef
Input source #2: Coordindates	5v2g.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
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

None

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 (Å)
1:11:CYS:SG	4:1:ZBR:C8	unknown	unknown	n/a
2:11:CYS:SG	4:1:ZBR:C7	unknown	unknown	n/a
3:11:CYS:SG	4:1:ZBR:C9	unknown	unknown	n/a
1:20:SER:C	2:1:LYS:N	unknown	unknown	n/a
2:20:SER:C	3:1:LYS:N	unknown	unknown	n/a
1:1:LYS:N	3:20:SER:C	unknown	unknown	n/a

Non-standard residues

Chain_ID	Seq_ID	Comp_ID	Chem_comp_name	Experimental evidences
D	1	ZBR	1,3,5-tris(bromomethyl)benzene	None

Sequence alignments

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

--------10--------20
KNPEAEEITRCKKLLDDSSS
||||||||||||||||||||
KNPEAEEITRCKKLLDDSSS

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

--------10--------20
KNPEAEEITRCKKLLDDSSS
||||||||||||||||||||
KNPEAEEITRCKKLLDDSSS

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

--------10--------20
KNPEAEEITRCKKLLDDSSS
||||||||||||||||||||
KNPEAEEITRCKKLLDDSSS

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Sequence coverage (%)
A	A	20	100.0
B	B	20	100.0
C	C	20	100.0

Content subtype: combined_30267_5v2g.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	6		No information
1	Assigned chemical shifts	assigned_chemical_shifts_1	Warning	479		100.0 (chain: A, length: 20), 100.0 (chain: B, length: 20), 100.0 (chain: C, length: 20)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	459 (1)	noe	100.0 (chain: A, length: 20), 100.0 (chain: B, length: 20), 100.0 (chain: C, length: 20)

Assigned chemical shifts

Saveframe: assigned_chemical_shifts_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 20, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 20, Sequence coverage: 100.0%
  - Entity_assembly_ID: C, Chain length: 20, Sequence coverage: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 305
  - ¹³C chemical shifts: 174
- Completeness of assignments
  - Entity_assemble_ID: A
  - Entity_assemble_ID: B
  - Entity_assemble_ID: C
- Redox state of CYS
- Peptide bond of PRO
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A
  - Chain_ID: B
  - Chain_ID: C

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	122	95	77.9
¹³C chemical shifts	86	58	67.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	39	38	97.4
¹³C chemical shifts	40	20	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	83	57	68.7
¹³C chemical shifts	46	38	82.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	8	7	87.5
¹³C chemical shifts	8	8	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	122	94	77.0
¹³C chemical shifts	86	58	67.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	39	38	97.4
¹³C chemical shifts	40	20	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	83	56	67.5
¹³C chemical shifts	46	38	82.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	8	7	87.5
¹³C chemical shifts	8	8	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	122	95	77.9
¹³C chemical shifts	86	58	67.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	39	38	97.4
¹³C chemical shifts	40	20	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	83	57	68.7
¹³C chemical shifts	46	38	82.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	8	7	87.5
¹³C chemical shifts	8	8	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 20, Sequence coverage: 100.0%
  - Entity_assembly_ID: B, Chain length: 20, Sequence coverage: 100.0%
  - Entity_assembly_ID: C, Chain length: 20, Sequence coverage: 100.0%
- Total number of restraints: 459
- Weight of restraints: 1.0 (459)
- Potential type of restraints: square-well-parabolic (459)
- Range of distance target values: 2.0, 3.65 (Å)
- 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
    None
- Distance restraints on contact map

Keywords Covalent Constrained peptide, DE NOVO PROTEIN, De Novo Design

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.615 seconds)

BMRB: 30267

Sample

Related entities 1. 20-mer Peptide, : 2 entities Detail

Experiments performed 4 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 3 contents Detail