SMTL ID : 8g4m.1

Vaccine-elicited human antibody 2C06 in complex with HIV-1 envelope trimer BG505 DS-SOSIP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

3 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[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.1: 10 residues within 4Å: Chain A: E.57, N.58 Chain B: G.16, S.17 Chain G: G.55, D.56, S.57, T.58, Y.59, Y.60 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:Y.60 NAG-NAG-BMA-MAN-MAN.15: 10 residues within 4Å: Chain C: E.57, N.58 Chain D: G.16, S.17 Chain K: G.55, D.56, S.57, T.58, Y.59, Y.60 2 PLIP interactions: 2 interactions with chain K Hydrophobic interactions: K:Y.60 Hydrogen bonds: K:G.55 NAG-NAG-BMA-MAN-MAN.29: 11 residues within 4Å: Chain E: E.57, N.58 Chain F: G.16, S.17 Chain I: G.55, D.56, S.57, T.58, Y.59, Y.60, T.69 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:Y.60, I:T.69

36 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: 1 residues within 4Å: Chain A: N.103 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain A: R.162, N.167 Chain C: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 6 residues within 4Å: Chain A: Q.263, N.265, N.301, S.303, R.412, V.414 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 7 residues within 4Å: Chain A: N.265, T.267, H.299, N.301, S.381, T.383, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 7 residues within 4Å: Chain A: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG.11, NAG-NAG.11 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG-NAG.10, NAG-NAG.10, NAG-NAG.12 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain A: G.358, N.361 Ligands: NAG-NAG.11, NAG-NAG.11 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain A: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.5 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 5 residues within 4Å: Chain A: T.98, Q.100, S.120, F.121, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain C: N.103, G.114, K.117, Y.161 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 5 residues within 4Å: Chain C: V.104, N.106, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain C: R.162, N.167 Chain E: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain C: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 7 residues within 4Å: Chain C: Q.263, N.265, N.301, V.302, S.303, S.381, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain C: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 6 residues within 4Å: Chain C: N.265, T.267, H.299, N.301, T.383, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 7 residues within 4Å: Chain C: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG.25, NAG-NAG.25 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 5 residues within 4Å: Chain C: N.355, S.357 Ligands: NAG-NAG.24, NAG-NAG.24, NAG-NAG.26 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain C: N.361 Ligands: NAG-NAG.25, NAG-NAG.25 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 4 residues within 4Å: Chain C: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.19 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 5 residues within 4Å: Chain C: Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 3 residues within 4Å: Chain E: N.103, G.114, K.117 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 4 residues within 4Å: Chain E: V.104, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 3 residues within 4Å: Chain A: R.278 Chain E: R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 4 residues within 4Å: Chain E: N.204, T.206, S.244, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 3 residues within 4Å: Chain E: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 7 residues within 4Å: Chain E: Q.263, N.265, N.301, S.303, R.412, V.414 Ligands: NAG-NAG.38 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 3 residues within 4Å: Chain E: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 8 residues within 4Å: Chain E: N.265, T.267, H.299, N.301, S.381, T.383, R.412 Ligands: NAG-NAG.36 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 7 residues within 4Å: Chain E: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG.40, NAG-NAG.40 No protein-ligand interaction detected (PLIP) NAG-NAG.40: 5 residues within 4Å: Chain E: N.355, S.357 Ligands: NAG-NAG.39, NAG-NAG.39, NAG-NAG.41 No protein-ligand interaction detected (PLIP) NAG-NAG.41: 2 residues within 4Å: Chain E: N.361 Ligands: NAG-NAG.40 No protein-ligand interaction detected (PLIP) NAG-NAG.42: 4 residues within 4Å: Chain E: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.34 No protein-ligand interaction detected (PLIP) NAG-NAG.43: 5 residues within 4Å: Chain E: Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP)

1 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: V.104, N.106, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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.5: 13 residues within 4Å: Chain A: S.179, E.181, P.182, V.224, L.231, N.232, N.346, G.348, Q.408, C.413, V.414, S.415 Ligands: NAG-NAG.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.414 NAG-NAG-BMA-MAN-MAN-MAN.34: 12 residues within 4Å: Chain E: K.177, S.179, E.181, P.182, V.224, L.231, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG.42 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.19: 11 residues within 4Å: Chain C: S.179, E.181, P.182, V.224, L.231, N.232, G.348, C.413, V.414, S.415 Ligands: NAG-NAG.27 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.414

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

NAG.44: 5 residues within 4Å: Chain A: N.204, T.206, S.244, I.247, H.321 No protein-ligand interaction detected (PLIP) NAG.45: 2 residues within 4Å: Chain A: N.308, W.364 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.308 NAG.46: 1 residues within 4Å: Chain A: N.324 No protein-ligand interaction detected (PLIP) NAG.47: 2 residues within 4Å: Chain B: E.123, N.126 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.126 NAG.48: 4 residues within 4Å: Chain C: N.204, T.206, S.244, H.321 No protein-ligand interaction detected (PLIP) NAG.49: 3 residues within 4Å: Chain C: K.304, N.308, W.364 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.308 NAG.50: 1 residues within 4Å: Chain C: N.324 No protein-ligand interaction detected (PLIP) NAG.51: 2 residues within 4Å: Chain D: N.126, Y.127 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.126, D:Y.127 NAG.52: 2 residues within 4Å: Chain E: N.308, W.364 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.308 NAG.53: 1 residues within 4Å: Chain E: N.324 No protein-ligand interaction detected (PLIP) NAG.54: 2 residues within 4Å: Chain F: N.100, S.102 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.102 NAG.55: 3 residues within 4Å: Chain F: E.123, N.126, Y.127 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, S. et al., HIV-1 neutralizing antibodies elicited in humans by a prefusion-stabilized envelope trimer form a reproducible class targeting fusion peptide. Cell Rep (2023)

Release Date

2023-07-12

Peptides

Envelope glycoprotein gp120: ACE
Envelope glycoprotein gp41: BDF
antibody heavy chain: GIK
antibody light chain: HJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
G

E
I

B
A

D
B

F
F

G
D

I
H

K
J

H
E

J
L

L
K

Envelope glycoprotein gp120

Envelope glycoprotein gp41

antibody heavy chain

antibody light chain

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