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

MHC CLASS I NATURAL MUTANT H-2KBM1 HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND SENDAI VIRUS NUCLEOPROTEIN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-2-2-mer

Ligands

2 x PHE- ALA- PRO- GLY- ASN- TYR- PRO- ALA- LEU: PROTEIN (NUCLEOCAPSID PROTEIN)(Non-covalent)

PHE-ALA-PRO-GLY-ASN-TYR-PRO-ALA-LEU.1: 23 residues within 4Å: Chain A: Y.7, V.9, Y.45, R.62, E.63, K.66, N.70, F.74, D.77, T.80, L.81, Y.84, S.99, Q.114, Y.116, Y.123, T.143, K.146, W.147, Y.159, T.163, W.167, Y.171 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:Y.7, A:F.74, A:F.74, A:Y.123, A:T.143, A:Y.159, A:T.163, A:W.167, A:W.167 Hydrogen bonds: A:Y.7, A:Y.7, A:E.63, A:K.66, A:N.70, A:S.73, A:D.77, A:S.99, A:S.99, A:Y.171 Water bridges: A:N.70, A:D.77, A:T.80 Salt bridges: A:K.146 pi-Cation interactions: A:K.66 PHE-ALA-PRO-GLY-ASN-TYR-PRO-ALA-LEU.9: 23 residues within 4Å: Chain C: Y.7, V.9, Y.45, R.62, E.63, K.66, N.70, F.74, D.77, T.80, L.81, Y.84, S.99, Q.114, Y.116, Y.123, T.143, K.146, W.147, Y.159, T.163, W.167, Y.171 24 PLIP interactions: 24 interactions with chain C Hydrophobic interactions: C:Y.7, C:F.74, C:F.74, C:Y.123, C:T.143, C:Y.159, C:T.163, C:W.167, C:W.167 Hydrogen bonds: C:Y.7, C:Y.7, C:E.63, C:K.66, C:N.70, C:S.73, C:D.77, C:S.99, C:S.99, C:Y.171 Water bridges: C:N.70, C:D.77, C:T.80 Salt bridges: C:K.146 pi-Cation interactions: C:K.66

2 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 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.54, A:K.173, A:N.174, A:N.174, A:N.176 NAG-NAG-FUL.10: 4 residues within 4Å: Chain C: Q.54, K.173, N.174, N.176 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.54, C:K.173, C:N.174, C:N.174, C:N.176

2 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 Hydrogen bonds: A:N.86 NAG.11: 1 residues within 4Å: Chain C: N.86 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.86

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

PO4.4: 3 residues within 4Å: Chain A: R.108, R.169 Chain C: Y.262 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain C Water bridges: A:E.161, A:R.169, A:R.169 Salt bridges: A:R.108, A:R.169 Hydrogen bonds: C:Y.262 PO4.5: 5 residues within 4Å: Chain A: V.12, R.14, R.21 Chain B: H.34 Ligands: MRD.6 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Water bridges: A:R.21 Salt bridges: A:R.14, A:R.21, B:H.34 PO4.12: 3 residues within 4Å: Chain A: Y.262 Chain C: R.108, R.169 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain A Water bridges: C:E.161, C:R.169, C:R.169 Salt bridges: C:R.108, C:R.169 Hydrogen bonds: A:Y.262 PO4.13: 5 residues within 4Å: Chain C: V.12, R.14, R.21 Chain D: H.34 Ligands: MRD.14 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain D Water bridges: C:R.21 Salt bridges: C:R.14, C:R.21, D:H.34

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

MRD.6: 7 residues within 4Å: Chain A: R.21, M.23 Chain B: F.30, P.33, M.54, I.64 Ligands: PO4.5 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.21 Hydrophobic interactions: B:F.30, B:I.64 Water bridges: B:H.34, B:I.35 MRD.14: 7 residues within 4Å: Chain C: R.21, M.23 Chain D: F.30, P.33, M.54, I.64 Ligands: PO4.13 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.30, D:I.64 Water bridges: D:H.34, D:I.35 Hydrogen bonds: C:R.21

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

MPD.7: 4 residues within 4Å: Chain A: P.47, R.48, A.49, R.50 No protein-ligand interaction detected (PLIP) MPD.8: 8 residues within 4Å: Chain A: H.188, T.190, W.204 Chain B: S.11, H.13, P.14, P.15, M.99 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:W.204 Hydrogen bonds: B:S.11, B:M.99 MPD.15: 4 residues within 4Å: Chain C: P.47, R.48, A.49, R.50 No protein-ligand interaction detected (PLIP) MPD.16: 8 residues within 4Å: Chain C: H.188, T.190, W.204 Chain D: S.11, H.13, P.14, P.15, M.99 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.11, D:M.99 Hydrophobic interactions: C:W.204

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: AC
PROTEIN (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

PROTEIN (BETA-2-MICROGLOBULIN)

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