SMTL ID : 7bh8.1

3H4-Fab HLA-E-VL9 co-complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

2 x VAL- MET- ALA- PRO- ARG- THR- VAL- LEU- LEU: VL9 leader peptide(Non-covalent)

VAL-MET-ALA-PRO-ARG-THR-VAL-LEU-LEU.1: 31 residues within 4Å: Chain A: Y.7, H.9, M.45, Y.59, R.62, E.63, S.66, A.67, T.70, I.73, F.74, N.77, T.80, L.81, Y.84, L.95, W.97, H.99, F.116, W.133, S.143, K.146, E.152, H.155, Q.156, Y.159, T.163, W.167, Y.171 Chain E: S.124, Y.125 34 PLIP interactions: 31 interactions with chain A, 3 interactions with chain E Hydrophobic interactions: A:Y.7, A:Y.59, A:I.73, A:L.81, A:L.95, A:W.97, A:F.116, A:W.133, A:E.152, A:H.155, A:Y.159, A:T.163, A:W.167, E:Y.125, E:Y.125 Hydrogen bonds: A:Y.7, A:E.63, A:N.77, A:N.77, A:H.99, A:E.152, A:Q.156, A:Y.171, A:Y.171, E:Y.120 Water bridges: A:R.62, A:S.66, A:N.77, A:T.80, A:K.146, A:E.152 Salt bridges: A:K.146, A:E.152 pi-Cation interactions: A:H.155 VAL-MET-ALA-PRO-ARG-THR-VAL-LEU-LEU.2: 33 residues within 4Å: Chain C: Y.7, H.9, M.45, Y.59, R.62, E.63, S.66, A.67, T.70, I.73, F.74, V.76, N.77, T.80, L.81, Y.84, W.97, H.99, F.116, L.124, W.133, S.143, K.146, S.147, E.152, H.155, Q.156, Y.159, T.163, W.167, Y.171 Chain G: S.124, Y.125 32 PLIP interactions: 30 interactions with chain C, 2 interactions with chain G Hydrophobic interactions: C:Y.59, C:V.76, C:L.81, C:W.97, C:F.116, C:L.124, C:W.133, C:Y.159, C:T.163, C:W.167, G:Y.125, G:Y.125 Hydrogen bonds: C:Y.7, C:E.63, C:N.77, C:N.77, C:Y.84, C:H.99, C:S.143, C:E.152, C:Q.156, C:Y.159, C:Y.171 Water bridges: C:R.62, C:E.63, C:S.66, C:T.80, C:E.152, C:E.152 Salt bridges: C:K.146, C:E.152 pi-Cation interactions: C:H.155

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: F.8, Y.27, D.29, D.30 Chain B: Y.64 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:Y.64 Hydrogen bonds: A:D.30 GOL.4: 4 residues within 4Å: Chain A: T.31, T.178, Y.209, G.239 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.178 GOL.5: 6 residues within 4Å: Chain A: K.6, E.102, R.111, Y.113, Q.115 Chain B: K.59 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.6, A:K.6, A:E.102, A:R.111 Water bridges: A:Q.115 GOL.6: 11 residues within 4Å: Chain A: W.204, L.206, R.234, Q.242 Chain B: Y.11, S.12, R.13, H.14, P.15, R.98, M.100 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.12, B:H.14, B:R.98, B:M.100, A:R.234, A:Q.242, A:Q.242 GOL.7: 5 residues within 4Å: Chain B: S.34, D.35, I.36, H.52, L.65 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.34, B:D.35, B:D.35, B:I.36 Water bridges: B:S.53, B:L.55 GOL.8: 6 residues within 4Å: Chain C: T.31, T.178, L.179, Y.209, D.238, G.239 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:T.31, C:D.238 GOL.9: 7 residues within 4Å: Chain E: T.49, D.50, Y.51, N.52, N.71, P.72, N.73 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:T.49, E:Y.51, E:N.73 GOL.11: 8 residues within 4Å: Chain F: Q.56, K.58, L.66, P.78, R.80, F.81, E.100, D.101 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:Q.56, F:R.80, F:E.100 GOL.12: 4 residues within 4Å: Chain F: A.163, K.164, V.165, E.180 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:V.165, F:V.165 Water bridges: F:V.165, F:S.178 GOL.13: 4 residues within 4Å: Chain H: A.163, K.164, V.165, E.180 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:V.165, H:V.165 Water bridges: H:V.165

1 x CA: CALCIUM ION(Non-covalent)

CA.10: 5 residues within 4Å: Chain E: Y.120, Y.121, S.123, G.126 Chain F: Y.110 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:S.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, D. et al., Mouse and human antibodies bind HLA-E-leader peptide complexes and enhance NK cell cytotoxicity. Commun Biol (2022)

Release Date

2022-04-13

Peptides

HLA class I histocompatibility antigen, alpha chain E: AC
Beta-2-microglobulin: BD
3H4 Fab heavy chain: EG
3H4 Fab light chain: FH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

E
G

G
E

F
H

H
F

HLA class I histocompatibility antigen, alpha chain E

Beta-2-microglobulin

3H4 Fab heavy chain

3H4 Fab light chain

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