SMTL ID : 6v8x.1

VRC01 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

3 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: N.330, S.331, T.339 Ligands: NAG-NAG-BMA.3, NAG-NAG-BMA.3 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.13: 5 residues within 4Å: Chain E: N.330, S.331, T.339 Ligands: NAG-NAG-BMA.15, NAG-NAG-BMA.15 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.25: 5 residues within 4Å: Chain I: N.330, S.331, T.339 Ligands: NAG-NAG-BMA.27, NAG-NAG-BMA.27 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 3 residues within 4Å: Chain A: S.355, G.356, N.359 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 7 residues within 4Å: Chain A: Q.261, N.263, N.299, V.300, S.379, R.410 Ligands: NAG-NAG.11 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain A: Q.98, S.118, N.120, K.131 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain A: V.142, R.160, N.165, T.166 Chain I: R.276 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain A: E.55, N.56 Chain B: S.9 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 6 residues within 4Å: Chain A: T.265, N.299, S.379, T.381, R.410 Ligands: NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain A: N.269, I.290, V.408 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain E: S.355, G.356, N.359 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 7 residues within 4Å: Chain E: Q.261, N.263, N.299, V.300, S.379, R.410 Ligands: NAG-NAG.23 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain E: Q.98, S.118, N.120, K.131 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain A: R.276 Chain E: V.142, R.160, N.165, T.166 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain E: E.55, N.56 Chain F: S.9 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 6 residues within 4Å: Chain E: T.265, N.299, S.379, T.381, R.410 Ligands: NAG-NAG.18 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain E: N.269, I.290, V.408 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain I: S.355, G.356, N.359 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 7 residues within 4Å: Chain I: Q.261, N.263, N.299, V.300, S.379, R.410 Ligands: NAG-NAG.35 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 4 residues within 4Å: Chain I: Q.98, S.118, N.120, K.131 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 5 residues within 4Å: Chain E: R.276 Chain I: V.142, R.160, N.165, T.166 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 3 residues within 4Å: Chain I: E.55, N.56 Chain J: S.9 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 6 residues within 4Å: Chain I: T.265, N.299, S.379, T.381, R.410 Ligands: NAG-NAG.30 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 3 residues within 4Å: Chain I: N.269, I.290, V.408 No protein-ligand interaction detected (PLIP)

12 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.3: 5 residues within 4Å: Chain A: N.353, S.355 Ligands: NAG-NAG-BMA-MAN.1, NAG-NAG-BMA-MAN.1, NAG-NAG-BMA-MAN.1 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 7 residues within 4Å: Chain A: L.229, N.230, G.346, C.411, V.412, S.413 Ligands: NAG.37 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.346 NAG-NAG-BMA.5: 7 residues within 4Å: Chain A: N.244 Chain D: Y.26, G.27, S.28, W.63, G.64, Y.87 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.27 NAG-NAG-BMA.8: 3 residues within 4Å: Chain A: N.116, Y.133, D.288 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 5 residues within 4Å: Chain E: N.353, S.355 Ligands: NAG-NAG-BMA-MAN.13, NAG-NAG-BMA-MAN.13, NAG-NAG-BMA-MAN.13 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 7 residues within 4Å: Chain E: L.229, N.230, G.346, C.411, V.412, S.413 Ligands: NAG.42 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.346 NAG-NAG-BMA.17: 7 residues within 4Å: Chain E: N.244 Chain H: Y.26, G.27, S.28, W.63, G.64, Y.87 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:G.27 NAG-NAG-BMA.20: 3 residues within 4Å: Chain E: N.116, Y.133, D.288 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 5 residues within 4Å: Chain I: N.353, S.355 Ligands: NAG-NAG-BMA-MAN.25, NAG-NAG-BMA-MAN.25, NAG-NAG-BMA-MAN.25 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.28: 7 residues within 4Å: Chain I: L.229, N.230, G.346, C.411, V.412, S.413 Ligands: NAG.47 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:G.346 NAG-NAG-BMA.29: 7 residues within 4Å: Chain I: N.244 Chain L: Y.26, G.27, S.28, W.63, G.64, Y.87 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:G.27 NAG-NAG-BMA.32: 3 residues within 4Å: Chain I: N.116, Y.133, D.288 No protein-ligand interaction detected (PLIP)

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

NAG.37: 4 residues within 4Å: Chain A: P.259, V.412, N.414 Ligands: NAG-NAG-BMA.4 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain A: N.322 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain A: N.101, K.115 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain A: N.306, E.307, W.362 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain B: N.92, S.94 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain E: P.259, V.412, N.414 Ligands: NAG-NAG-BMA.16 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain E: N.322 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain E: N.101, K.115 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain E: N.306, E.307, W.362 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain F: N.92, S.94 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain I: P.259, V.412, N.414 Ligands: NAG-NAG-BMA.28 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain I: N.322 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain I: N.101, K.115 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain I: N.306, E.307, W.362 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain J: N.92, S.94 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Henderson, R. et al., Disruption of the HIV-1 Envelope allosteric network blocks CD4-induced rearrangements. Nat Commun (2020)

Release Date

2020-02-05

Peptides

Envelope glycoprotein gp120: AEI
Envelope glycoprotein gp41: BFJ
VRC01 Fab Heavy Chain: CGK
VRC01 Fab Light Chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

I
I

B
B

F
F

J
J

C
C

G
G

K
K

D
D

H
H

L
L

Envelope glycoprotein gp120

Envelope glycoprotein gp41

VRC01 Fab Heavy Chain

VRC01 Fab Light Chain

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