SMTL ID : 7kdp.1

HCMV prefusion gB in complex with fusion inhibitor WAY-174865

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-trimer

Ligands

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

NAG.1: 4 residues within 4Å: Chain A: W.174, Y.186, S.188, N.208 Ligand excluded by PLIP NAG.2: 3 residues within 4Å: Chain A: N.281, T.283, N.284 Ligand excluded by PLIP NAG.3: 1 residues within 4Å: Chain A: N.286 Ligand excluded by PLIP NAG.4: 2 residues within 4Å: Chain A: P.301, N.302 Ligand excluded by PLIP NAG.5: 1 residues within 4Å: Chain A: N.341 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.383, S.385 Ligand excluded by PLIP NAG.7: 3 residues within 4Å: Chain A: Q.401, F.404, N.405 Ligand excluded by PLIP NAG.8: 2 residues within 4Å: Chain A: G.416, N.417 Ligand excluded by PLIP NAG.9: 7 residues within 4Å: Chain A: N.555, T.557, N.583, F.584, A.585, N.586, S.587 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.220, N.586 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain B: W.174, Y.186, S.188, N.208 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain B: N.281, T.283, N.284 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain B: N.286 Ligand excluded by PLIP NAG.17: 2 residues within 4Å: Chain B: P.301, N.302 Ligand excluded by PLIP NAG.18: 1 residues within 4Å: Chain B: N.341 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.383, S.385 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain B: Q.401, F.404, N.405 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: G.416, N.417 Ligand excluded by PLIP NAG.22: 7 residues within 4Å: Chain B: N.555, T.557, N.583, F.584, A.585, N.586, S.587 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain B: N.220, N.586 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain C: W.174, Y.186, S.188, N.208 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain C: N.281, T.283, N.284 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain C: N.286 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: P.301, N.302 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain C: N.341 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: N.383, S.385 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain C: Q.401, F.404, N.405 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain C: G.416, N.417 Ligand excluded by PLIP NAG.33: 7 residues within 4Å: Chain C: N.555, T.557, N.583, F.584, A.585, N.586, S.587 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain C: N.220, N.586 Ligand excluded by PLIP

3 x WCY: N-{4-[({(1S)-1-[3,5-bis(trifluoromethyl)phenyl]ethyl}carbamothioyl)amino]phenyl}-1,3-thiazole-4-carboxamide(Non-covalent)

WCY.11: 14 residues within 4Å: Chain A: Y.153, Y.155, F.747, N.750, F.752, G.753 Chain C: G.711, L.712, D.714, L.715, I.730, G.731, G.734, G.735 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:D.714, C:I.730 Hydrogen bonds: C:L.715 WCY.13: 14 residues within 4Å: Chain A: G.711, L.712, D.714, L.715, I.730, G.731, G.734, G.735 Chain B: Y.153, Y.155, F.747, N.750, F.752, G.753 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:D.714, A:I.730 Hydrogen bonds: A:L.715 WCY.24: 14 residues within 4Å: Chain B: G.711, L.712, D.714, L.715, I.730, G.731, G.734, G.735 Chain C: Y.153, Y.155, F.747, N.750, F.752, G.753 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:D.714, B:I.730 Hydrogen bonds: B:L.715

1 x CA: CALCIUM ION(Non-functional Binders)

CA.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, Y. et al., Prefusion structure of human cytomegalovirus glycoprotein B and structural basis for membrane fusion. Sci Adv (2021)

Release Date

2021-03-17

Peptides

Envelope glycoprotein B: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Membrane

We predict this structure to be a membrane protein.
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Envelope glycoprotein B

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