SMTL ID : 4osu.1

Crystal structure of HCMV gB-neutralizing SM5-1 Fab fragment

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.87 Å

Oligo State

hetero-oligomer

Ligands

7 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 7 residues within 4Å: Chain A: N.116, R.117 Chain B: Y.33, V.34, S.35, F.50, D.51 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:D.51, A:N.116, A:N.116 Water bridges: B:S.35 FMT.2: 4 residues within 4Å: Chain A: Y.33, W.50, N.52, L.112 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.52 Water bridges: A:Y.33, A:S.55 FMT.3: 3 residues within 4Å: Chain A: Y.60, Q.65, G.66 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.65, A:G.66 FMT.6: 2 residues within 4Å: Chain B: S.25, S.26 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.26 FMT.7: 3 residues within 4Å: Chain A: A.186 Chain B: T.165, T.166 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.166, B:T.166 FMT.8: 2 residues within 4Å: Chain B: P.112, K.113 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.113, B:K.113 FMT.9: 4 residues within 4Å: Chain A: P.141 Chain B: S.124, S.125, E.126 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.125, B:E.126 Water bridges: B:S.125

2 x NA: SODIUM ION(Non-functional Binders)

NA.4: 2 residues within 4Å: Chain A: E.10, K.19 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.10, A:K.19 Water bridges: A:E.10 NA.5: 1 residues within 4Å: Chain A: T.103 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.103 Water bridges: A:T.103

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Spindler, N. et al., Structural basis for the recognition of human cytomegalovirus glycoprotein B by a neutralizing human antibody. Plos Pathog. (2014)

Release Date

2014-08-13

Peptides

SM5-1 Fab Heavy Chain: A
SM5-1 Fab Light Chain: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

SM5-1 Fab Heavy Chain

SM5-1 Fab Light Chain

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