SMTL ID : 1fzm.1

MHC CLASS I NATURAL MUTANT H-2KBM8 HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND VESICULAR STOMATITIS VIRUS NUCLEOPROTEIN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

1 x ARG- GLY- TYR- VAL- TYR- GLN- GLY- LEU: PROTEIN (NUCLEOCAPSID PROTEIN)(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, 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, T.163, W.167, Y.171 38 PLIP interactions: 38 interactions with chain A Hydrophobic interactions: A:K.66, A:F.74, A:D.77, A:L.81, A:Y.116, A:W.147, A:Y.159, A:Y.159, A:Y.159, A:T.163, A:W.167 Hydrogen bonds: A:Y.7, A:R.62, A:E.63, A:K.66, A:N.70, A:N.70, A:D.77, A:S.99, A:S.99, A:E.152, A:E.152, A:R.155, A:R.155, A:Y.171, A:Y.171 Water bridges: A:S.73, A:S.73, A:S.73, A:S.73, A:D.77, A:T.80, A:Y.116, A:E.152, A:Y.159, A:Y.159 Salt bridges: A:E.63, A:K.146

1 x NAG- NAG- FUL: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

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

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

NAG.3: 1 residues within 4Å: Chain A: N.86 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.86

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

PO4.4: 6 residues within 4Å: Chain A: R.35, R.48 Chain B: V.49, E.50, M.51 Ligands: MRD.5 6 PLIP interactions: 4 interactions with chain A, 2 interactions with chain B Water bridges: A:R.48, A:R.48 Salt bridges: A:R.35, A:R.48 Hydrogen bonds: B:V.49, B:M.51 PO4.7: 6 residues within 4Å: Chain A: I.23 Chain B: P.33, I.35, M.54, I.64 Ligands: MRD.5 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Salt bridges: A:R.21 Water bridges: B:P.33, B:I.35, B:I.35

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.5: 11 residues within 4Å: Chain A: I.23, V.25, E.32, R.35, D.37 Chain B: M.51, S.52, D.53, M.54 Ligands: PO4.4, PO4.7 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.23, A:V.25, A:R.35, B:M.51 Hydrogen bonds: A:R.35, A:D.37, A:D.37, B:M.54

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

MPD.6: 5 residues within 4Å: Chain A: P.47, R.48, A.49, R.50, E.53 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.53 MPD.8: 12 residues within 4Å: Chain A: H.188, W.204, L.206, Q.242 Chain B: V.9, 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, A:L.206 Hydrogen bonds: B:S.11, B:S.11, B:H.13

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rudolph, M.G. et al., The crystal structures of K(bm1) and K(bm8) reveal that subtle changes in the peptide environment impact thermostability and alloreactivity. Immunity (2001)

Release Date

2001-03-28

Peptides

H-2 CLASS I HISTOCOMPATIBILITY ANTIGEN, K-B ALPHA CHAIN: A
PROTEIN (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

PROTEIN (BETA-2-MICROGLOBULIN)

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