SMTL ID : 5c6t.1

Crystal structure of HCMV glycoprotein B in complex with 1G2 Fab

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.60 Å

Oligo State

hetero-3-3-3-mer

Ligands

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 5 residues within 4Å: Chain A: N.219, N.222, A.225, R.258 Chain C: S.57 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain D: N.219, N.222, A.225, R.258 Chain F: S.57 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain G: N.219, N.222, A.225, R.258 Chain I: S.57 No protein-ligand interaction detected (PLIP)

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

NAG.2: 2 residues within 4Å: Chain A: N.343, T.344 Ligand excluded by PLIP NAG.3: 7 residues within 4Å: Chain A: W.112, Y.124, S.126, S.128, V.137, Y.139, N.146 Ligand excluded by PLIP NAG.4: 2 residues within 4Å: Chain A: N.321, S.323 Ligand excluded by PLIP NAG.5: 1 residues within 4Å: Chain A: N.355 Ligand excluded by PLIP NAG.6: 1 residues within 4Å: Chain A: N.224 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.279 Ligand excluded by PLIP NAG.8: 4 residues within 4Å: Chain A: N.493, T.495, S.496, N.521 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain A: N.240 Chain C: Q.54 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain D: N.343, T.344 Ligand excluded by PLIP NAG.13: 7 residues within 4Å: Chain D: W.112, Y.124, S.126, S.128, V.137, Y.139, N.146 Ligand excluded by PLIP NAG.14: 2 residues within 4Å: Chain D: N.321, S.323 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain D: N.355 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain D: N.224 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain D: N.279 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain D: N.493, T.495, S.496, N.521 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain D: N.240 Chain F: Q.54 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain G: N.343, T.344 Ligand excluded by PLIP NAG.23: 7 residues within 4Å: Chain G: W.112, Y.124, S.126, S.128, V.137, Y.139, N.146 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain G: N.321, S.323 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain G: N.355 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain G: N.224 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain G: N.279 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain G: N.493, T.495, S.496, N.521 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain G: N.240 Chain I: Q.54 Ligand excluded by PLIP

3 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 5 residues within 4Å: Chain A: D.447 Chain D: D.447 Chain G: D.447 Ligands: MG.20, MG.30 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain G, 2 interactions with chain A Metal complexes: D:D.447, G:D.447, G:D.447, A:D.447, A:D.447 MG.20: 5 residues within 4Å: Chain A: D.447 Chain D: D.447 Chain G: D.447 Ligands: MG.10, MG.30 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain G, 2 interactions with chain A Metal complexes: D:D.447, G:D.447, G:D.447, A:D.447, A:D.447 MG.30: 5 residues within 4Å: Chain A: D.447 Chain D: D.447 Chain G: D.447 Ligands: MG.10, MG.20 5 PLIP interactions: 1 interactions with chain D, 2 interactions with chain G, 2 interactions with chain A Metal complexes: D:D.447, G:D.447, G:D.447, A:D.447, A:D.447

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chandramouli, S. et al., Structure of HCMV glycoprotein B in the postfusion conformation bound to a neutralizing human antibody. Nat Commun (2015)

Release Date

2015-09-23

Peptides

Envelope glycoprotein B: ADG
1G2 Fab heavy chain: BEH
1G2 Fab light chain: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

B
H

E
H

H
H

C
L

F
L

I
L

Envelope glycoprotein B

1G2 Fab heavy chain

1G2 Fab light chain