SMTL ID : 5cxf.1

Crystal structure of the extracellular domain of glycoprotein B from Human Cytomegalovirus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.60 Å

Oligo State

homo-trimer

Ligands

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN.1: 5 residues within 4Å: Chain A: W.97, Y.109, S.111, S.113, N.131 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.2: 5 residues within 4Å: Chain B: W.97, Y.109, S.111, S.113, N.131 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.3: 3 residues within 4Å: Chain B: N.306, S.308, D.309 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 2 residues within 4Å: Chain B: N.332, T.334 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 1 residues within 4Å: Chain B: N.509 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain C: N.204, T.206, N.207, D.261 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain C: N.478, T.480, A.508, N.509 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.6: 5 residues within 4Å: Chain C: W.97, Y.109, S.111, Y.124, N.131 No protein-ligand interaction detected (PLIP)

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

NAG.9: 3 residues within 4Å: Chain A: N.204, T.206, D.261 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.225, T.241 Ligand excluded by PLIP NAG.11: 2 residues within 4Å: Chain A: R.243, N.264 Ligand excluded by PLIP NAG.12: 1 residues within 4Å: Chain A: N.306 Ligand excluded by PLIP NAG.13: 1 residues within 4Å: Chain A: N.340 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: N.478, N.509, S.510 Ligand excluded by PLIP NAG.15: 1 residues within 4Å: Chain A: N.509 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain B: N.209 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.225 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain B: N.340 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: N.478, T.480, N.509 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain C: N.209 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain C: N.225 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain C: N.306, S.308 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain C: R.277, N.332, T.334 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain C: N.340 Ligand excluded by PLIP

1 x CA: CALCIUM ION(Non-covalent)

CA.16: 3 residues within 4Å: Chain A: D.432 Chain B: D.432 Chain C: D.432 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 2 interactions with chain B Metal complexes: A:D.432, A:D.432, C:D.432, B:D.432, B:D.432

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Burke, H.G. et al., Crystal Structure of the Human Cytomegalovirus Glycoprotein B. Plos Pathog. (2015)

Release Date

2015-10-28

Peptides

Envelope glycoprotein B: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Envelope glycoprotein B