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SMTL ID : 3spv.1

Crystal structure of a peptide-HLA complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ARG- ALA- LYS- PHE- LYS- GLN- LEU- LEU: peptide from Trans-activator protein BZLF1(Non-covalent)

ARG-ALA-LYS-PHE-LYS-GLN-LEU-LEU.1:

31 residues within 4Å:

Chain A: M.5, Y.7, D.9, R.62, N.63, I.66, F.67, T.69, N.70, T.73, D.74, E.76, S.77, N.80, Y.84, L.95, S.97, Y.99, N.114, Y.123, T.143, K.146, W.147, V.152, Q.155, D.156, Y.159, T.163, W.167, Y.171
Ligands: NA.4

41 PLIP interactions:

41 interactions with chain A

Hydrophobic interactions: A:I.66, A:I.66, A:F.67, A:N.70, A:E.76, A:L.95, A:Y.99, A:Y.123, A:W.147, A:V.152, A:Y.159, A:Y.159, A:Y.159, A:W.167
Hydrogen bonds: A:N.63, A:N.70, A:N.70, A:D.74, A:S.77, A:N.80, A:S.97, A:Y.99, A:Y.99, A:N.114, A:T.143, A:Q.155, A:D.156, A:Y.159, A:Y.171
Water bridges: A:Y.7, A:R.62, A:R.62, A:R.62, A:R.62, A:S.77, A:Y.116, A:Y.116, A:W.147, A:Q.155, A:W.167
Salt bridges: A:K.146

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.2:	5 residues within 4Å: Chain A: M.12, R.14, R.17, R.21 Chain B: D.34 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.14, A:R.17 Hydrogen bonds: B:D.34
ACT.3:	4 residues within 4Å: Chain A: S.92, H.93, D.119 Chain B: I.1 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Water bridges: B:I.1, A:Q.87, A:D.119, A:D.119 Salt bridges: A:H.93

1 x NA: SODIUM ION(Non-functional Binders)

NA.4:

7 residues within 4Å:

Chain A: D.9, A.11, D.74, L.95, Q.96, S.97
Ligands: ARG-ALA-LYS-PHE-LYS-GLN-LEU-LEU.1

3 PLIP interactions:

3 interactions with chain A

Hydrogen bonds: A:D.9, A:A.11
Water bridges: A:S.97

Links

RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP

Citation

Gras, S. et al., Crystal structure of a peptide-HLA complex. To be Published

Release Date

2012-07-04

Peptides

HLA class I histocompatibility antigen, B-8 alpha chain: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Export Alignment

Secondary Structure
NoneDSSPPSIPREDSSpro

Colour Scheme

Fade MismatchesEnhance Mismatches

ChainUnique ChainRainbow2° StructureBfactorBfactor RangeSOAEntropyClustalHydrophobicSizeChargedPolarProlineSer/ThrCysteineAliphaticAromaticNo Colour

Background

3D Viewer
NGLPV2D

HLA class I histocompatibility antigen, B-8 alpha chain

Beta-2-microglobulin

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