SMTL ID : 8g4t.1

Vaccine-elicited human antibody 2C09 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: 9 residues within 4Å: Chain A: G.16, S.17 Chain C: E.57, N.58 Chain I: G.56, S.57, T.58, Y.59, Y.60 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:G.56, I:Y.60 NAG-NAG-BMA-MAN-MAN.16: 9 residues within 4Å: Chain B: G.16, S.17 Chain E: E.57, N.58 Chain K: G.56, S.57, T.58, Y.59, Y.60 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:G.56, K:Y.60 NAG-NAG-BMA-MAN-MAN.31: 8 residues within 4Å: Chain D: G.16, S.17 Chain F: N.58 Chain G: G.56, S.57, T.58, Y.59, Y.60 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:G.56, G:Y.60

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: 2 residues within 4Å: Chain C: N.103, K.117 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain C: V.104, N.118, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain C: R.162, N.167 Chain E: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: N.204, T.206, S.244, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain C: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 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.9: 3 residues within 4Å: Chain C: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain C: T.267, H.299, N.301, T.383, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain C: N.332 Ligands: NAG-NAG.12, NAG-NAG.12 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain C: N.355, S.357 Ligands: NAG-NAG.11, NAG-NAG.11, NAG-NAG.13 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain C: N.361 Ligands: NAG-NAG.12 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain C: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.6 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain E: N.103, K.117 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain E: V.104, N.118, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain E: R.162, N.167 Chain F: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain E: N.204, T.206, S.244, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain E: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 5 residues within 4Å: Chain E: Q.263, N.265, S.303, S.381, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain E: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 5 residues within 4Å: Chain E: T.267, H.299, N.301, T.383, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 4 residues within 4Å: Chain E: N.332, S.333 Ligands: NAG-NAG.27, NAG-NAG.27 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 5 residues within 4Å: Chain E: N.355, S.357 Ligands: NAG-NAG.26, NAG-NAG.26, NAG-NAG.28 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 2 residues within 4Å: Chain E: N.361 Ligands: NAG-NAG.27 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 4 residues within 4Å: Chain E: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.21 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 2 residues within 4Å: Chain F: N.103, K.117 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 3 residues within 4Å: Chain F: V.104, N.118, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 3 residues within 4Å: Chain C: R.278 Chain F: R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 4 residues within 4Å: Chain F: N.204, T.206, S.244, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 3 residues within 4Å: Chain F: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 5 residues within 4Å: Chain F: Q.263, N.265, N.301, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 3 residues within 4Å: Chain F: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.40: 4 residues within 4Å: Chain F: H.299, N.301, T.383, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.41: 3 residues within 4Å: Chain F: N.332 Ligands: NAG-NAG.42, NAG-NAG.42 No protein-ligand interaction detected (PLIP) NAG-NAG.42: 5 residues within 4Å: Chain F: N.355, S.357 Ligands: NAG-NAG.41, NAG-NAG.41, NAG-NAG.43 No protein-ligand interaction detected (PLIP) NAG-NAG.43: 2 residues within 4Å: Chain F: N.361 Ligands: NAG-NAG.42 No protein-ligand interaction detected (PLIP) NAG-NAG.44: 4 residues within 4Å: Chain F: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.36 No protein-ligand interaction detected (PLIP)

3 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.6: 10 residues within 4Å: Chain C: S.179, E.181, V.224, L.231, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG.14 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.414 NAG-NAG-BMA-MAN-MAN-MAN.21: 9 residues within 4Å: Chain E: S.179, E.181, L.231, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG.29 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:V.414 NAG-NAG-BMA-MAN-MAN-MAN.36: 9 residues within 4Å: Chain F: S.179, E.181, V.224, L.231, N.232, G.348, V.414, S.415 Ligands: NAG-NAG.44 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.15: 5 residues within 4Å: Chain C: Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 5 residues within 4Å: Chain E: Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.45: 5 residues within 4Å: Chain F: Q.100, S.120, F.121, N.122, K.133 No protein-ligand interaction detected (PLIP)

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

NAG.46: 2 residues within 4Å: Chain A: N.100, S.102 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain A: N.107, S.109, E.110 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain A: K.122, E.123, N.126 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain B: N.100, S.102 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain B: N.107, S.109, E.110 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain B: K.122, E.123, N.126 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain C: N.324 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain C: N.308 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain D: N.100, S.102 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain D: N.107, S.109, E.110 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain D: K.122, E.123, N.126 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain E: N.324 Ligand excluded by PLIP NAG.58: 1 residues within 4Å: Chain E: N.308 Ligand excluded by PLIP NAG.59: 1 residues within 4Å: Chain F: N.324 Ligand excluded by PLIP NAG.60: 1 residues within 4Å: Chain F: N.308 Ligand excluded by 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 BG505 DS-SOSIP gp41: ABD
Envelope glycoprotein BG505 DS-SOSIP gp120: CEF
Fab 2C09 heavy chain: GIK
Fab 2C09 light chain: HJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
F

C
C

E
G

F
I

G
H

I
D

K
J

H
L

J
E

L
K

Envelope glycoprotein BG505 DS-SOSIP gp41

Envelope glycoprotein BG505 DS-SOSIP gp120

Fab 2C09 heavy chain

Fab 2C09 light chain

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