SMTL ID : 6mvl.1

Crystal structure of VISTA bound to a pH-selective antibody Fab fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.61 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

NAG.1: 3 residues within 4Å: Chain A: G.16, N.18, R.103 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.18

14 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: R.43, R.46, Q.60, L.108 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:Q.60 Water bridges: A:R.43, A:R.46, A:R.59, A:R.59, A:Q.60 Salt bridges: A:R.43, A:R.46 SO4.3: 4 residues within 4Å: Chain A: R.43, S.45, R.46, R.56 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:R.46 Water bridges: A:R.46, A:R.46, A:R.56, A:R.56 Salt bridges: A:R.43, A:R.46, A:R.56 SO4.4: 3 residues within 4Å: Chain A: H.124, S.125, H.127 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.125 Salt bridges: A:H.124, A:H.127 SO4.5: 3 residues within 4Å: Chain A: L.82, R.85, H.86 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.85, A:H.86 SO4.6: 3 residues within 4Å: Chain B: T.117, M.118, P.159 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.117, B:T.117, B:M.118 Water bridges: B:P.159, B:K.211 SO4.7: 3 residues within 4Å: Chain B: L.11, S.125, T.126 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.126, B:T.126 SO4.8: 2 residues within 4Å: Chain B: K.127, G.128 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.128 SO4.9: 4 residues within 4Å: Chain B: T.141, S.142, G.143, G.144 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.144 Water bridges: B:G.143, B:G.143, B:S.196 SO4.10: 2 residues within 4Å: Chain B: K.16, S.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.17, B:S.17 SO4.11: 1 residues within 4Å: Chain B: R.220 2 PLIP interactions: 2 interactions with chain B Water bridges: B:R.220 Salt bridges: B:R.220 SO4.12: 2 residues within 4Å: Chain C: R.55, S.64 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:S.53, C:S.64 Water bridges: C:S.64 Salt bridges: C:R.55 SO4.13: 4 residues within 4Å: Chain B: P.133 Chain C: S.122, D.123, E.124 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.122, C:D.123, C:E.124 SO4.14: 3 residues within 4Å: Chain C: K.40, Q.43, R.46 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Q.43 Water bridges: C:R.46, C:R.46 Salt bridges: C:K.40, C:R.46 SO4.15: 4 residues within 4Å: Chain A: Y.38, H.67, L.68 Chain C: Y.50 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.38 Water bridges: A:Y.38

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johnston, R.J. et al., VISTA is an acidic pH-selective ligand for PSGL-1. Nature (2019)

Release Date

2019-10-23

Peptides

V-type immunoglobulin domain-containing suppressor of T-cell activation: A
Antibody Fab fragment heavy chain: B
Antibody Fab fragment light chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
H

C
L

V-type immunoglobulin domain-containing suppressor of T-cell activation

Antibody Fab fragment heavy chain

Antibody Fab fragment light chain