SMTL ID : 5vcl.1

Structure of the Qdm peptide bound to Qa-1a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ALA- MET- ALA- PRO- ARG- THR- LEU- LEU- LEU: Qdm peptide(Non-covalent)

ALA-MET-ALA-PRO-ARG-THR-LEU-LEU-LEU.1: 29 residues within 4Å: Chain A: Y.8, H.10, M.46, E.64, K.67, A.68, M.71, N.74, F.75, N.78, T.81, Y.85, L.96, W.98, Y.100, E.117, I.125, W.134, S.144, K.147, S.148, V.151, E.153, Q.156, Q.157, Y.160, W.168, Y.172 Ligands: NA.7 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:N.74, A:L.96, A:W.98, A:Y.100, A:I.125, A:W.134, A:W.168 Hydrogen bonds: A:E.64, A:K.67, A:N.78, A:Y.100, A:S.144, A:V.151, A:Q.157, A:Y.172, A:Y.172 Water bridges: A:E.64, A:S.148 Salt bridges: A:K.147, A:E.153

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 6 residues within 4Å: Chain A: R.7, F.9, Y.28, D.30, D.31 Chain B: Y.63 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.7, A:D.31, B:Y.63, B:Y.63 Water bridges: A:S.5, A:D.30 GOL.3: 7 residues within 4Å: Chain A: L.110, L.111, R.112, G.113, E.129, L.131, Q.162 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.113, A:G.113, A:Q.162 GOL.4: 7 residues within 4Å: Chain A: Y.86, Y.119, Q.122, D.123, Y.124, T.137, D.138 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.86, A:Y.119, A:T.137, A:D.138 GOL.11: 7 residues within 4Å: Chain A: V.232, R.235 Chain B: Q.8, V.9, Y.94, D.96, M.99 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.8, B:V.9, B:V.9, B:Y.94, B:D.96, A:R.235

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

NA.5: 3 residues within 4Å: Chain A: D.30, L.180, Y.210 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.30, A:D.30 NA.6: 4 residues within 4Å: Chain A: F.9, T.11, I.24 Chain B: M.54 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.11 NA.7: 5 residues within 4Å: Chain A: F.75, N.78, E.117 Ligands: ALA-MET-ALA-PRO-ARG-THR-LEU-LEU-LEU.1, ALA-MET-ALA-PRO-ARG-THR-LEU-LEU-LEU.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.117 NA.8: 4 residues within 4Å: Chain A: Y.100, C.115, Q.157, Y.160 No protein-ligand interaction detected (PLIP) NA.9: 2 residues within 4Å: Chain A: S.3, E.265 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.3 NA.10: 4 residues within 4Å: Chain A: R.15, R.22, S.39, D.40 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.15, A:R.15, A:S.39

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ying, G. et al., Crystal structure of Qa-1a with bound Qa-1 determinant modifier peptide. PLoS ONE (2017)

Release Date

2017-10-25

Peptides

H2-T23 protein: A
Beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

H2-T23 protein

Beta-2-microglobulin

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