SMTL ID : 7sd3.1

Cytoplasmic tail deleted HIV-1 Env bound with three 4E10 Fabs

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-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: 10 residues within 4Å: Chain G: E.181, L.231, N.232, F.345, N.346, G.348, C.413, V.414, S.415 Ligands: NAG.14 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:E.181 Hydrogen bonds: G:E.181, G:E.181, G:G.348 NAG-NAG-BMA.3: 2 residues within 4Å: Chain G: G.323, N.324 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 10 residues within 4Å: Chain I: E.181, L.231, N.232, F.345, N.346, G.348, C.413, V.414, S.415 Ligands: NAG.26 4 PLIP interactions: 4 interactions with chain I Hydrophobic interactions: I:E.181 Hydrogen bonds: I:E.181, I:E.181, I:G.348 NAG-NAG-BMA.6: 2 residues within 4Å: Chain I: G.323, N.324 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 10 residues within 4Å: Chain K: E.181, L.231, N.232, F.345, N.346, G.348, C.413, V.414, S.415 Ligands: NAG.38 4 PLIP interactions: 4 interactions with chain K Hydrophobic interactions: K:E.181 Hydrogen bonds: K:E.181, K:E.181, K:G.348 NAG-NAG-BMA.9: 2 residues within 4Å: Chain K: G.323, N.324 No protein-ligand interaction detected (PLIP)

3 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: 4 residues within 4Å: Chain G: N.204, T.206, P.208, H.321 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:T.206 NAG-NAG.5: 4 residues within 4Å: Chain I: N.204, T.206, P.208, H.321 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:T.206 NAG-NAG.8: 4 residues within 4Å: Chain K: N.204, T.206, P.208, H.321 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:T.206

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

NAG.10: 5 residues within 4Å: Chain G: Q.100, S.120, F.121, N.122, K.133 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain G: N.103 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain G: N.271, V.410 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain G: N.265, T.267, H.299, N.301 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain G: P.261, N.416 Ligands: NAG-NAG-BMA.1 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain G: S.357, F.360, N.361 Ligand excluded by PLIP NAG.16: 1 residues within 4Å: Chain G: N.355 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain G: E.57, N.58 Chain H: S.17 Ligand excluded by PLIP NAG.18: 5 residues within 4Å: Chain G: V.104, N.118, Y.135, L.137, D.290 Ligand excluded by PLIP NAG.19: 1 residues within 4Å: Chain H: N.114 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain H: N.107, S.109, E.110 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain H: N.126 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain I: Q.100, S.120, F.121, N.122, K.133 Ligand excluded by PLIP NAG.23: 1 residues within 4Å: Chain I: N.103 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain I: N.271, V.410 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain I: N.265, T.267, H.299, N.301 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain I: P.261, N.416 Ligands: NAG-NAG-BMA.4 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain I: S.357, F.360, N.361 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain I: N.355 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain I: E.57, N.58 Chain J: S.17 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain I: V.104, N.118, Y.135, L.137, D.290 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain J: N.114 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain J: N.107, S.109, E.110 Ligand excluded by PLIP NAG.33: 1 residues within 4Å: Chain J: N.126 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain K: Q.100, S.120, F.121, N.122, K.133 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain K: N.103 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain K: N.271, V.410 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain K: N.265, T.267, H.299, N.301 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain K: N.232, P.261, N.416 Ligands: NAG-NAG-BMA.7 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain K: S.357, F.360, N.361 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain K: N.355 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain K: E.57, N.58 Chain L: S.17 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain K: V.104, N.118, Y.135, L.137, D.290 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain L: N.114 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain L: N.107, S.109, E.110 Ligand excluded by PLIP NAG.45: 1 residues within 4Å: Chain L: N.126 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, S. et al., Dynamic HIV-1 spike motion creates vulnerability for its membrane-bound tripod to antibody attack. Nat Commun (2022)

Release Date

2022-11-09

Peptides

4E10 Fab light chain: ACE
4E10 Fab heavy chain: BDF
Envelope glycoprotein gp120: GIK
Transmembrane protein gp41: HJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

C
N

E
M

B
G

D
K

F
I

G
A

I
C

K
E

H
B

J
D

L
F

4E10 Fab light chain

4E10 Fab heavy chain

Envelope glycoprotein gp120

Transmembrane protein gp41

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