SMTL ID : 6vo0.1

BG505 SOSIP.v5.2 in complex with rabbit Fab 43A2

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

18 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 B: D.54 Chain C: N.103 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:D.54 Hydrogen bonds: B:D.54 NAG-NAG.2: 4 residues within 4Å: Chain C: Q.100, S.120, F.121, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain C: Q.263, N.265, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: N.232, P.261, N.416 Ligands: NAG-NAG-BMA.3 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain C: V.104, N.106, N.118, Y.135, L.137 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.135 NAG-NAG.7: 3 residues within 4Å: Chain A: H.27 Chain C: N.106, N.107 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain F: D.54 Chain G: N.103 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:D.54 Hydrogen bonds: F:D.54 NAG-NAG.9: 4 residues within 4Å: Chain G: Q.100, S.120, F.121, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain G: Q.263, N.265, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain G: N.232, P.261, N.416 Ligands: NAG-NAG-BMA.10 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain G: V.104, N.106, N.118, Y.135, L.137 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:Y.135 NAG-NAG.14: 3 residues within 4Å: Chain E: H.27 Chain G: N.106, N.107 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain J: D.54 Chain K: N.103 2 PLIP interactions: 2 interactions with chain J Hydrophobic interactions: J:D.54 Hydrogen bonds: J:D.54 NAG-NAG.16: 4 residues within 4Å: Chain K: Q.100, S.120, F.121, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain K: Q.263, N.265, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain K: N.232, P.261, N.416 Ligands: NAG-NAG-BMA.17 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 5 residues within 4Å: Chain K: V.104, N.106, N.118, Y.135, L.137 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:Y.135 NAG-NAG.21: 3 residues within 4Å: Chain I: H.27 Chain K: N.106, N.107 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.3: 10 residues within 4Å: Chain C: E.181, K.222, V.224, L.231, N.232, C.347, C.413, V.414, S.415 Ligands: NAG-NAG.5 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:V.414 Hydrogen bonds: C:V.414 NAG-NAG-BMA.10: 10 residues within 4Å: Chain G: E.181, K.222, V.224, L.231, N.232, C.347, C.413, V.414, S.415 Ligands: NAG-NAG.12 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:V.414 Hydrogen bonds: G:V.414 NAG-NAG-BMA.17: 10 residues within 4Å: Chain K: E.181, K.222, V.224, L.231, N.232, C.347, C.413, V.414, S.415 Ligands: NAG-NAG.19 2 PLIP interactions: 2 interactions with chain K Hydrophobic interactions: K:V.414 Hydrogen bonds: K:V.414

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

NAG.22: 4 residues within 4Å: Chain C: N.246, I.247, T.248 Ligands: NAG.28 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain C: N.271, I.292, V.410 Ligand excluded by PLIP NAG.24: 5 residues within 4Å: Chain C: N.265, T.267, H.299, N.301, R.412 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain C: T.342, N.355, S.357, R.387 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain C: S.357, N.361 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain C: N.332, S.333, S.334 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain C: N.204, T.206, I.247 Ligands: NAG.22 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain C: R.162, N.167, T.168 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain C: E.57, N.58 Chain D: G.16, S.17 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain G: N.246, I.247, T.248 Ligands: NAG.37 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain G: N.271, I.292, V.410 Ligand excluded by PLIP NAG.33: 5 residues within 4Å: Chain G: N.265, T.267, H.299, N.301, R.412 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain G: T.342, N.355, S.357, R.387 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain G: S.357, N.361 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain G: N.332, S.333, S.334 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain G: N.204, T.206, I.247 Ligands: NAG.31 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain G: R.162, N.167, T.168 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain G: E.57, N.58 Chain H: G.16, S.17 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain K: N.246, I.247, T.248 Ligands: NAG.46 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain K: N.271, I.292, V.410 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain K: N.265, T.267, H.299, N.301, R.412 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain K: T.342, N.355, S.357, R.387 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain K: S.357, N.361 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain K: N.332, S.333, S.334 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain K: N.204, T.206, I.247 Ligands: NAG.40 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain K: R.162, N.167, T.168 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain K: E.57, N.58 Chain L: G.16, S.17 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nogal, B. et al., HIV envelope trimer-elicited autologous neutralizing antibodies bind a region overlapping the N332 glycan supersite. Sci Adv (2020)

Release Date

2020-07-01

Peptides

43A2 light chain: AEI
43A2 heavy chain: BFJ
Envelope glycoprotein gp120: CGK
Envelope glycoprotein gp41: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

E
J

I
K

B
H

F
G

J
I

C
A

G
C

K
D

D
B

H
E

L
F

43A2 light chain

43A2 heavy chain

Envelope glycoprotein gp120

Envelope glycoprotein gp41

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