SMTL ID : 1kpu.1

High resolution crystal structure of the MHC class I complex H-2Kb/VSV8

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ARG- GLY- TYR- VAL- TYR- GLN- GLY- LEU: nucleocapsid(Non-covalent)

ARG-GLY-TYR-VAL-TYR-GLN-GLY-LEU.1: 24 residues within 4Å: Chain A: Y.7, V.9, R.62, E.63, K.66, N.70, S.73, F.74, D.77, T.80, L.81, Y.84, S.99, Q.114, Y.116, T.143, K.146, W.147, E.152, R.155, L.156, Y.159, W.167, Y.171 34 PLIP interactions: 34 interactions with chain A Hydrophobic interactions: A:V.9, A:K.66, A:F.74, A:Y.116, A:T.143, A:W.147, A:L.156, A:Y.159, A:Y.159 Hydrogen bonds: A:Y.7, A:Y.7, A:R.62, A:E.63, A:K.66, A:N.70, A:N.70, A:S.73, A:D.77, A:S.99, A:S.99, A:E.152, A:E.152, A:R.155, A:R.155, A:W.167, A:Y.171 Water bridges: A:E.63, A:D.77, A:T.80, A:Y.116, A:E.152, A:Y.159, A:Y.159 Salt bridges: A:K.146

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.2: 4 residues within 4Å: Chain A: Q.54, K.173, N.174, N.176 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.54, A:N.174 Water bridges: A:N.174

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.3: 1 residues within 4Å: Chain A: N.86 No protein-ligand interaction detected (PLIP)

2 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 3 residues within 4Å: Chain A: A.135, A.136, D.137 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.136 Water bridges: A:A.136 MPD.5: 7 residues within 4Å: Chain A: T.10, V.12, R.21 Chain B: F.30, P.33, M.54, I.64 8 PLIP interactions: 5 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.30, B:I.64, A:T.10, A:V.12 Hydrogen bonds: B:P.33, A:R.21 Water bridges: B:H.34, B:I.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rudolph, M.G. et al., High Resolution Crystal Structure of H-2Kb/VSV8. To be Published

Release Date

2003-06-10

Peptides

H-2 class I histocompatibility antigen, K-B alpha chain: A
beta-2-microglobulin: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

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

beta-2-microglobulin

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