SMTL ID : 8tqa.1

Crystal structure of Fab.28.14.8 in complex with MHC-I (H2-Db)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x ALA- SER- ASN- GLU- ASN- MET- GLU- THR- MET: influenza peptide(Non-covalent)

ALA-SER-ASN-GLU-ASN-MET-GLU-THR-MET.1: 26 residues within 4Å: Chain A: M.4, Y.6, Y.44, E.62, K.65, G.68, Q.69, W.72, S.76, N.79, L.80, Y.83, L.94, F.115, T.142, K.145, W.146, S.149, H.154, Y.155, Y.158, E.162, W.166, Y.170 Ligands: GOL.4, EDO.13 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:W.72, A:L.80, A:T.142, A:K.145, A:Y.155, A:Y.158, A:W.166 Hydrogen bonds: A:Y.44, A:Y.44, A:E.62, A:Q.69, A:Q.69, A:S.76, A:N.79, A:K.145, A:Y.158, A:E.162, A:Y.170 Salt bridges: A:K.145

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: R.5, F.7, Y.112, Q.114 Chain B: K.58 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.5, A:Q.114, B:K.58 GOL.4: 9 residues within 4Å: Chain A: Y.6, E.8, S.98, L.113, Y.155, Y.158 Ligands: ALA-SER-ASN-GLU-ASN-MET-GLU-THR-MET.1, ALA-SER-ASN-GLU-ASN-MET-GLU-THR-MET.1, ALA-SER-ASN-GLU-ASN-MET-GLU-THR-MET.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.8, A:S.98, A:Y.155, A:Y.158 Water bridges: A:Q.69

9 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 8 residues within 4Å: Chain A: D.211, T.213, Y.261, H.262, E.263 Chain C: Y.50, Y.57, E.59 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:Y.50, A:T.213, A:T.213, A:E.263, A:E.263 EDO.5: 5 residues within 4Å: Chain A: F.7, Y.26, N.29 Chain B: F.56, Y.63 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.63 EDO.6: 7 residues within 4Å: Chain A: W.203, R.233, Q.241 Chain B: S.11, R.12, H.13, P.14 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.233, B:M.99 EDO.8: 6 residues within 4Å: Chain A: E.221 Chain C: Y.102, D.104 Chain D: Y.49, H.55, S.56 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:Y.49, D:S.56, C:Y.102, C:D.104 EDO.9: 3 residues within 4Å: Chain A: N.219 Chain D: Y.50, S.52 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.52 EDO.10: 3 residues within 4Å: Chain D: N.31, S.65, G.66 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.66 EDO.11: 6 residues within 4Å: Chain D: Q.37, K.45, P.59, F.62, E.81, D.82 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Q.37, D:K.45, D:E.81, D:E.81 EDO.12: 5 residues within 4Å: Chain D: T.85, G.100, G.101, T.102, K.103 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.85, D:T.85, D:G.100 EDO.13: 3 residues within 4Å: Ligands: ALA-SER-ASN-GLU-ASN-MET-GLU-THR-MET.1, ALA-SER-ASN-GLU-ASN-MET-GLU-THR-MET.1, ALA-SER-ASN-GLU-ASN-MET-GLU-THR-MET.1 No protein-ligand interaction detected (PLIP)

1 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG.7: 1 residues within 4Å: Chain C: N.28 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.28, C:N.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Boyd, L.F. et al., Experimental Structures of Antibody/MHC-I Complexes Reveal Details of Epitopes Overlooked by Computational Prediction. J Immunol. (2024)

Release Date

2024-03-20

Peptides

H-2 class I histocompatibility antigen, D-B alpha chain: A
Beta-2-microglobulin: B
Fab.28.14S Heavy chain: C
Fab.28.14S Light Chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
H

D
L

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

Beta-2-microglobulin

Fab.28.14S Heavy chain

Fab.28.14S Light Chain

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