SMTL ID : 6v8z.1

VRC03 and 10-1074 Bound BG505 F14 HIV-1 SOSIP Envelope Trimer Structure

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-3-3-mer

Ligands

27 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: 2 residues within 4Å: Chain A: E.56, N.57 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.331 Ligands: NAG-NAG.4, NAG-NAG.4 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.354, S.356 Ligands: NAG-NAG.3, NAG.40 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: N.231, P.260, N.415 Ligands: NAG-NAG-BMA-MAN.9 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: Q.262, N.264, S.302, R.411 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: N.270, T.272, V.409 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain A: R.161, L.162, I.163, C.165, N.166 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain A: V.103, N.117, Y.134, I.290 Chain D: R.90 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.134 NAG-NAG.12: 4 residues within 4Å: Chain A: N.102, I.107, K.116, R.139 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain G: E.56, N.57 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain G: N.331 Ligands: NAG-NAG.16, NAG-NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain G: N.354, S.356 Ligands: NAG-NAG.15, NAG.47 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain G: N.231, P.260, N.415 Ligands: NAG-NAG-BMA-MAN.21 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain G: Q.262, N.264, S.302, R.411 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain G: N.270, T.272, V.409 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 5 residues within 4Å: Chain G: R.161, L.162, I.163, C.165, N.166 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 5 residues within 4Å: Chain G: V.103, N.117, Y.134, I.290 Chain J: R.90 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:Y.134 NAG-NAG.24: 4 residues within 4Å: Chain G: N.102, I.107, K.116, R.139 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 2 residues within 4Å: Chain M: E.56, N.57 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain M: N.331 Ligands: NAG-NAG.28, NAG-NAG.28 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 4 residues within 4Å: Chain M: N.354, S.356 Ligands: NAG-NAG.27, NAG.54 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 4 residues within 4Å: Chain M: N.231, P.260, N.415 Ligands: NAG-NAG-BMA-MAN.33 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 4 residues within 4Å: Chain M: Q.262, N.264, S.302, R.411 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 3 residues within 4Å: Chain M: N.270, T.272, V.409 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 5 residues within 4Å: Chain M: R.161, L.162, I.163, C.165, N.166 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 5 residues within 4Å: Chain M: V.103, N.117, Y.134, I.290 Chain P: R.90 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:Y.134 NAG-NAG.36: 4 residues within 4Å: Chain M: N.102, I.107, K.116, R.139 No protein-ligand interaction detected (PLIP)

3 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: 2 residues within 4Å: Chain A: N.203, T.205 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 2 residues within 4Å: Chain G: N.203, T.205 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.26: 2 residues within 4Å: Chain M: N.203, T.205 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-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-MAN-MAN-MAN.8: 14 residues within 4Å: Chain A: N.264, T.266, H.298, N.300, S.380, R.411 Chain C: R.103, I.104, G.106, V.107, V.108 Chain D: N.44, Q.45, P.59 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.20: 14 residues within 4Å: Chain G: N.264, T.266, H.298, N.300, S.380, R.411 Chain I: R.103, I.104, G.106, V.107, V.108 Chain J: N.44, Q.45, P.59 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.32: 14 residues within 4Å: Chain M: N.264, T.266, H.298, N.300, S.380, R.411 Chain O: R.103, I.104, G.106, V.107, V.108 Chain P: N.44, Q.45, P.59 1 PLIP interactions: 1 interactions with chain O Hydrogen bonds: O:V.108

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.9: 9 residues within 4Å: Chain A: K.34, E.180, P.181, N.231, N.345, C.346, V.413, S.414 Ligands: NAG-NAG.5 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.21: 9 residues within 4Å: Chain G: K.34, E.180, P.181, N.231, N.345, C.346, V.413, S.414 Ligands: NAG-NAG.17 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.33: 9 residues within 4Å: Chain M: K.34, E.180, P.181, N.231, N.345, C.346, V.413, S.414 Ligands: NAG-NAG.29 No protein-ligand interaction detected (PLIP)

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

NAG.37: 4 residues within 4Å: Chain A: N.245 Chain E: Y.111 Chain F: N.30, F.90 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain A: N.323 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain A: N.307, S.361 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain A: S.356, N.360 Ligands: NAG-NAG.4 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain B: N.120 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain B: N.94, S.96 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain B: N.101, S.103 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain G: N.245 Chain K: Y.111 Chain L: N.30, F.90 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain G: N.323 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain G: N.307, S.361 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain G: S.356, N.360 Ligands: NAG-NAG.16 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain H: N.120 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain H: N.94, S.96 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain H: N.101, S.103 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain M: N.245 Chain Q: Y.111 Chain R: N.30, F.90 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain M: N.323 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain M: N.307, S.361 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain M: S.356, N.360 Ligands: NAG-NAG.28 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain N: N.120 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain N: N.94, S.96 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain N: N.101, S.103 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: AGM
envelope glycoprotein gp41: BHN
10-1074 Fab Heavy Chain: CIO
10-1074 Fab Light Chain: DJP
VRC03 Fab Heavy Chain: EKQ
VRC03 Fab Light Chain: FLR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

G
G

M
M

B
B

H
H

N
N

C
D

I
J

O
P

D
E

J
K

P
Q

E
C

K
I

Q
O

F
F

L
L

R
R

Envelope glycoprotein gp120

envelope glycoprotein gp41

10-1074 Fab Heavy Chain

10-1074 Fab Light Chain

VRC03 Fab Heavy Chain

VRC03 Fab Light Chain

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