SMTL ID : 4huw.2 (1 other biounit)

Crystal Structure of H2Db-NPM6T

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.16 Å

Oligo State

hetero-2-2-mer

Ligands

2 x ALA- SER- ASN- GLU- ASN- THR- GLU- THR- MET: NPM6T variant peptide(Non-covalent)

ALA-SER-ASN-GLU-ASN-THR-GLU-THR-MET.1: 27 residues within 4Å: Chain C: M.6, Y.8, Y.46, Y.60, E.64, K.67, G.70, Q.71, W.74, F.75, V.77, S.78, N.81, Y.85, L.96, Q.98, F.117, T.144, K.147, W.148, S.151, A.153, H.156, Y.157, Y.160, W.168, Y.172 30 PLIP interactions: 30 interactions with chain C Hydrophobic interactions: C:K.67, C:W.74, C:V.77, C:H.156, C:Y.160, C:W.168 Hydrogen bonds: C:Y.8, C:Y.46, C:Y.46, C:Y.60, C:E.64, C:K.67, C:Q.71, C:Q.71, C:S.78, C:N.81, C:Q.98, C:Q.98, C:K.147, C:K.147, C:S.151, C:S.151, C:Y.157, C:Y.157, C:Y.172, C:Y.172 Water bridges: C:S.100, C:Y.160 Salt bridges: C:K.147, C:K.147 ALA-SER-ASN-GLU-ASN-THR-GLU-THR-MET.2: 29 residues within 4Å: Chain A: M.6, Y.8, Y.46, E.64, K.67, G.70, Q.71, W.74, F.75, V.77, S.78, N.81, L.82, Y.85, L.96, Q.98, F.117, Y.124, I.125, T.144, K.147, W.148, S.151, A.153, H.156, Y.157, Y.160, W.168, Y.172 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:K.67, A:W.74, A:V.77, A:L.82, A:K.147, A:H.156, A:Y.160, A:W.168 Hydrogen bonds: A:Y.46, A:Y.46, A:E.64, A:K.67, A:Q.71, A:Q.71, A:S.78, A:N.81, A:Y.85, A:Q.98, A:Q.98, A:T.144, A:S.151, A:S.151, A:S.151, A:H.156, A:Y.157, A:Y.157, A:Y.160, A:Y.172 Salt bridges: A:K.147, A:K.147

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

SO4.3: 4 residues within 4Å: Chain A: Q.88 Chain B: M.1 Chain C: Q.88 Chain D: M.1 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:M.1, C:Q.88, A:Q.88 SO4.4: 3 residues within 4Å: Chain C: R.112, Y.114 Chain D: K.59 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Y.114 Salt bridges: C:R.112, D:K.59

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
E

C
G

B
F

D
H

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

Beta-2-microglobulin

Related Entries With Identical Sequence