SMTL ID : 7t77.1

HIV-1 Envelope ApexGT3.N130 in complex with PG9 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

20 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: 5 residues within 4Å: Chain A: V.135, N.149, S.151, Y.166, D.315 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.166 Hydrogen bonds: A:Y.166 NAG-NAG.2: 3 residues within 4Å: Chain A: T.129, N.153 Ligands: NAG.34 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: V.175, R.187, L.188, I.189, N.192 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.175 NAG-NAG.4: 5 residues within 4Å: Chain A: F.228, N.229, T.231, P.233, H.346 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: Q.288, N.290, N.326, V.327 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: N.296, I.317, V.435 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 6 residues within 4Å: Chain A: N.290, T.292, H.324, N.326, T.408, R.437 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain A: Q.357, T.366, T.367, N.380, S.382 Ligands: NAG.32 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.357 NAG-NAG.9: 4 residues within 4Å: Chain A: N.257, S.440, N.441 Ligands: NAG-NAG-BMA-MAN-MAN.10 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain C: V.175, Q.176, R.187, N.192 Chain E: R.303 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 6 residues within 4Å: Chain C: N.290, T.292, H.324, N.326, T.408, R.437 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 7 residues within 4Å: Chain C: Q.357, T.366, T.367, N.380, S.382, R.412 Ligands: NAG.42 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.357 NAG-NAG.15: 5 residues within 4Å: Chain C: N.257, P.286, V.439, S.440, N.441 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 6 residues within 4Å: Chain C: N.134, V.135, T.136, N.149, Y.166, D.315 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.166 Hydrogen bonds: C:Y.166 NAG-NAG.18: 3 residues within 4Å: Chain C: N.131, S.151, S.184 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain E: N.296, I.317, V.435 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 6 residues within 4Å: Chain E: N.290, T.292, H.324, N.326, T.408, R.437 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain E: T.366, T.367, N.380, S.382 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 2 residues within 4Å: Chain E: S.382, N.386 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain E: N.257, N.441 Ligands: NAG-NAG-BMA.20 No protein-ligand interaction detected (PLIP)

1 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.10: 7 residues within 4Å: Chain A: E.206, N.257, N.371, C.438, V.439, S.440 Ligands: NAG-NAG.9 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.439 Hydrogen bonds: A:V.439

5 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.12: 7 residues within 4Å: Chain C: P.207, V.249, L.256, N.257, G.373, V.439, S.440 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.373 NAG-NAG-BMA.16: 4 residues within 4Å: Chain C: T.129, N.153 Chain E: N.160 Chain H: S.58 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.19: 2 residues within 4Å: Chain A: R.303 Chain E: N.192 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 7 residues within 4Å: Chain E: E.206, V.249, L.256, N.257, V.439, S.440 Ligands: NAG-NAG.25 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 3 residues within 4Å: Chain E: N.131, S.184 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.26 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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-MAN-MAN.26: 15 residues within 4Å: Chain E: T.129, N.131, F.152, N.153 Chain G: D.103, R.105, Y.110, Y.118, N.119, Y.120, H.121 Chain H: S.34, D.52, R.97 Ligands: NAG-NAG-BMA.27 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:Y.118

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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-MAN.28: 9 residues within 4Å: Chain E: V.135, T.136, N.137, N.149, Y.166 Chain G: D.72, N.73, S.74, Y.114 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:Y.114, G:Y.114

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

NAG.29: 2 residues within 4Å: Chain A: E.88, N.89 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain A: N.137, N.138, G.318, D.319 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: R.344, K.345, N.349 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: N.386 Ligands: NAG-NAG.8 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: N.271, I.272, T.273 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain A: N.131, S.151, S.184 Ligands: NAG-NAG.2, NAG-NAG.2 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: T.133, N.134, V.135 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain B: P.98, W.99, N.100, W.103 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain B: N.107 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain B: K.122, E.123, S.125, N.126 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain C: T.133, N.134, R.144, K.148 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: Q.288, N.290, N.326 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: G.348, N.349 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain C: Q.357, S.382, N.386 Ligands: NAG-NAG.14, NAG-NAG.14 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain C: N.271, T.273 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain C: F.228, N.229, G.230, T.231, G.232 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: N.296, I.317, V.435 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain C: N.89 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain C: S.179, N.180 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain D: N.100, S.101 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain D: N.105, R.106, N.107, S.109 Ligand excluded by PLIP NAG.50: 5 residues within 4Å: Chain D: K.122, E.123, S.125, N.126, Y.127 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain E: T.133, N.134, R.144 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain E: N.271, T.273 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain E: Q.288, N.290, N.326 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain E: R.344, F.347, G.348, N.349 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain E: S.453, T.454, N.455 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain E: N.89 Chain F: G.16 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain E: T.136, N.137, N.138 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain F: N.100, S.101 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain F: N.107, S.109, E.110 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain F: E.123, N.126, Y.127 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Willis, J.R. et al., Human immunoglobulin repertoire analysis guides design of vaccine priming immunogens targeting HIV V2-apex broadly neutralizing antibody precursors. Immunity (2022)

Release Date

2022-09-28

Peptides

HIV Envelope ApexGT3.N130 gp120: ACE
HIV Envelope ApexGT3.N130 gp41: BDF
PG9 Fab Heavy Chain: G
PG9 Fab Light Chain: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

G
H

H
L

HIV Envelope ApexGT3.N130 gp120

HIV Envelope ApexGT3.N130 gp41

PG9 Fab Heavy Chain

PG9 Fab Light Chain

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