SMTL ID : 5vod.2 (1 other biounit)

Crystal structure of HCMV Pentamer in complex with neutralizing antibody 9I6

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 5.90 Å

Oligo State

hetero-2-2-2-2-2-2-2-mer

Ligands

6 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.1: 2 residues within 4Å: Chain A: L.640, N.641 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 2 residues within 4Å: Chain A: N.192, Q.193 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 2 residues within 4Å: Chain D: N.201 Chain E: H.116 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 2 residues within 4Å: Chain H: L.640, N.641 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 2 residues within 4Å: Chain H: N.192, Q.193 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 2 residues within 4Å: Chain K: N.201 Chain L: H.116 No protein-ligand interaction detected (PLIP)

4 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.3: 3 residues within 4Å: Chain A: R.47, R.50, N.67 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.50, A:R.50 NAG-NAG-BMA-MAN-MAN.6: 5 residues within 4Å: Chain C: Y.130 Chain E: Y.52, N.81, E.84 Chain J: N.37 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain J Hydrogen bonds: E:Y.52, J:N.37 NAG-NAG-BMA-MAN-MAN.9: 3 residues within 4Å: Chain H: R.47, R.50, N.67 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:R.50, H:R.50 NAG-NAG-BMA-MAN-MAN.12: 5 residues within 4Å: Chain C: N.37 Chain J: Y.130 Chain L: Y.52, N.81, E.84 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.37

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

NAG-NAG.4: 4 residues within 4Å: Chain D: T.79, G.80, P.81, N.85 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.85 NAG-NAG.10: 4 residues within 4Å: Chain K: T.79, G.80, P.81, N.85 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:N.85

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chandramouli, S. et al., Structural basis for potent antibody-mediated neutralization of human cytomegalovirus. Sci Immunol (2017)

Release Date

2017-07-05

Peptides

Envelope glycoprotein H: AH
Envelope glycoprotein L: BI
Envelope glycoprotein UL128: CJ
Envelope glycoprotein UL130: DK
Envelope glycoprotein UL131A: EL
Fab 9I6 heavy chain: FM
Fab 9I6 light chain: GN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

H
A

B
B

I
B

C
C

J
C

D
D

K
D

E
E

L
E

F
H

M
H

G
L

N
L

Envelope glycoprotein H

Envelope glycoprotein L

Envelope glycoprotein UL128

Envelope glycoprotein UL130

Envelope glycoprotein UL131A

Fab 9I6 heavy chain

Fab 9I6 light chain

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