SMTL ID : 1kpv.2 (1 other biounit)

High resolution crystal structure of the MHC class I complex H-2Kb/SEV9

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

hetero-2-2-mer

Ligands

2 x PHE- ALA- PRO- GLY- ASN- TYR- PRO- ALA- LEU: Nucleocapsid protein(Non-covalent)

PHE-ALA-PRO-GLY-ASN-TYR-PRO-ALA-LEU.1: 24 residues within 4Å: Chain A: Y.7, V.9, Y.45, E.63, K.66, N.70, S.73, F.74, D.77, T.80, L.81, Y.84, S.99, Q.114, Y.116, Y.123, T.143, K.146, W.147, E.152, Y.159, T.163, W.167, Y.171 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:Y.7, A:F.74, A:F.74, A:D.77, A:L.81, A:Y.116, A:Y.123, A:T.143, A:W.147, A:E.152, A:Y.159, A:T.163, A:W.167 Hydrogen bonds: A:Y.7, A:Y.7, 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:Y.171 Water bridges: A:Y.45, A:K.66, A:N.70, A:D.77, A:T.80, A:Y.116, A:Y.116 Salt bridges: A:K.146 pi-Cation interactions: A:K.66 PHE-ALA-PRO-GLY-ASN-TYR-PRO-ALA-LEU.8: 24 residues within 4Å: Chain C: Y.7, V.9, Y.45, E.63, K.66, N.70, S.73, F.74, D.77, T.80, L.81, Y.84, S.99, Q.114, Y.116, Y.123, T.143, K.146, W.147, E.152, Y.159, T.163, W.167, Y.171 33 PLIP interactions: 33 interactions with chain C Hydrophobic interactions: C:Y.7, C:F.74, C:F.74, C:D.77, C:L.81, C:Y.116, C:Y.123, C:T.143, C:W.147, C:E.152, C:Y.159, C:T.163, C:W.167 Hydrogen bonds: C:Y.7, C:Y.7, C:E.63, C:K.66, C:N.70, C:N.70, C:S.73, C:D.77, C:S.99, C:S.99, C:Y.171 Water bridges: C:Y.45, C:K.66, C:N.70, C:D.77, C:T.80, C:Y.116, C:Y.116 Salt bridges: C:K.146 pi-Cation interactions: C:K.66

2 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:K.173, A:K.173 NAG-NAG-FUC.9: 4 residues within 4Å: Chain C: Q.54, K.173, N.174, N.176 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Q.54, C:K.173, C:K.173

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 5 residues within 4Å: Chain A: V.12, R.14, R.21 Chain B: H.34 Ligands: MPD.6 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Water bridges: A:R.21, A:R.21, B:H.34, B:H.34 Salt bridges: A:R.14, A:R.21, B:H.34 PO4.4: 3 residues within 4Å: Chain A: E.166, W.167, R.170 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.167 Water bridges: A:R.170, A:R.170 PO4.10: 5 residues within 4Å: Chain C: V.12, R.14, R.21 Chain D: H.34 Ligands: MPD.13 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain D Water bridges: C:R.21, C:R.21, D:H.34, D:H.34 Salt bridges: C:R.14, C:R.21, D:H.34 PO4.11: 3 residues within 4Å: Chain C: E.166, W.167, R.170 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:W.167 Water bridges: C:R.170, C:R.170

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

MPD.5: 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.6: 7 residues within 4Å: Chain A: T.10, V.12, R.21, M.23 Chain B: P.33, M.54 Ligands: PO4.3 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:T.10, A:V.12, A:R.21 Hydrogen bonds: B:P.33, B:I.35 Water bridges: B:H.34 MPD.7: 11 residues within 4Å: Chain A: H.188, W.204, L.206, Q.242 Chain B: Y.10, S.11, H.13, P.14, P.15, W.95, D.96 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.10, A:W.204 Hydrogen bonds: B:S.11, B:S.11, B:H.13, A:Q.242 MPD.12: 3 residues within 4Å: Chain C: A.135, A.136, D.137 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.136 Water bridges: C:A.136 MPD.13: 7 residues within 4Å: Chain C: T.10, V.12, R.21, M.23 Chain D: P.33, M.54 Ligands: PO4.10 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:P.33, D:I.35 Water bridges: D:H.34 Hydrophobic interactions: C:T.10, C:V.12, C:R.21 MPD.14: 11 residues within 4Å: Chain C: H.188, W.204, L.206, Q.242 Chain D: Y.10, S.11, H.13, P.14, P.15, W.95, D.96 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Y.10, C:W.204 Hydrogen bonds: D:S.11, D:S.11, D:H.13, C:Q.242

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: 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, K-B alpha chain

beta-2-microglobulin

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