SMTL ID : 4hv8.1 (1 other biounit)

Crystal Structure of H2Db-H155A-NPM6I

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-oligomer

Ligands

2 x ALA- SER- ASN- GLU- ASN- ILE- GLU- THR- MET: NPM6I variant peptide(Non-covalent)

ALA-SER-ASN-GLU-ASN-ILE-GLU-THR-MET.1: 25 residues within 4Å: Chain A: M.6, Y.8, Y.46, E.64, K.67, Q.71, W.74, F.75, V.77, S.78, N.81, L.82, Y.85, L.96, Q.98, F.117, Y.124, T.144, K.147, W.148, S.151, Y.157, Y.160, W.168, Y.172 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:K.67, A:W.74, A:V.77, A:Y.160, A:W.168 Hydrogen bonds: A:Y.46, A:E.64, A:K.67, A:Q.71, A:Q.71, A:S.78, A:N.81, A:Q.98, A:Q.98, A:K.147, A:S.151, A:S.151, A:Y.157, A:Y.172, A:Y.172 Water bridges: A:Y.8, A:S.25, A:Y.85, A:A.156, A:Y.157 Salt bridges: A:K.147, A:K.147 ALA-SER-ASN-GLU-ASN-ILE-GLU-THR-MET.6: 25 residues within 4Å: Chain C: M.6, Y.8, Y.46, E.64, K.67, Q.71, W.74, F.75, V.77, S.78, N.81, L.82, Y.85, L.96, Q.98, F.117, Y.124, T.144, K.147, W.148, S.151, Y.157, Y.160, W.168, Y.172 29 PLIP interactions: 29 interactions with chain C Hydrophobic interactions: C:K.67, C:W.74, C:V.77, C:Y.160, C:W.168 Hydrogen bonds: C:Y.8, C:Y.46, C:Y.46, C:E.64, C:K.67, C:Q.71, C:Q.71, C:S.78, C:N.81, C:Y.85, C:Q.98, C:Q.98, C:T.144, C:K.147, C:K.147, C:S.151, C:Y.160, C:Y.172 Water bridges: C:S.25, C:E.64, C:A.156, C:Y.157 Salt bridges: C:K.147, C:K.147

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: Q.142, R.146 Chain D: A.89, E.90 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:A.89, D:E.90, A:Q.142 Water bridges: D:K.84 Salt bridges: A:R.146 SO4.3: 3 residues within 4Å: Chain A: R.112, Y.114 Chain B: K.59 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Water bridges: B:K.59, B:K.59, B:K.59, A:R.112 Salt bridges: B:K.59, A:R.112 SO4.4: 2 residues within 4Å: Chain A: R.22 Chain B: M.55 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Water bridges: A:R.22, A:R.22, A:R.22, A:R.22 Salt bridges: A:R.22 Hydrogen bonds: B:M.55 SO4.5: 4 residues within 4Å: Chain B: R.13, I.23, E.51, H.68 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.51 Salt bridges: B:R.13, B:H.68 SO4.7: 4 residues within 4Å: Chain B: A.89, E.90 Chain C: Q.142, R.146 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:Q.142, B:A.89 Salt bridges: C:R.146 Water bridges: B:K.84 SO4.8: 3 residues within 4Å: Chain C: R.112, Y.114 Chain D: K.59 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Water bridges: D:K.59, D:K.59, D:K.59, C:R.112 Salt bridges: D:K.59, C:R.112 Hydrogen bonds: C:Y.114 SO4.9: 2 residues within 4Å: Chain C: R.22 Chain D: M.55 6 PLIP interactions: 2 interactions with chain D, 4 interactions with chain C Hydrogen bonds: D:M.55 Water bridges: D:D.54, C:R.22, C:R.22, C:R.22 Salt bridges: C:R.22 SO4.10: 4 residues within 4Å: Chain D: R.13, I.23, E.51, H.68 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.51 Salt bridges: D:R.13, D:H.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Valkenburg, S.A. et al., Preemptive priming readily overcomes structure-based mechanisms of virus escape. Proc.Natl.Acad.Sci.USA (2013)

Release Date

2013-02-27

Peptides

H-2 class I histocompatibility antigen, D-B alpha chain: AC
Beta-2-microglobulin: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

H-2 class I histocompatibility antigen, D-B alpha chain

Beta-2-microglobulin

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