SMTL ID : 7t76.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

22 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: 6 residues within 4Å: Chain A: V.135, N.149, Y.166, L.168, G.314, D.315 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.166 NAG-NAG.2: 3 residues within 4Å: Chain A: S.151, F.152, N.153 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 2 residues within 4Å: Chain A: R.187, N.192 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.187 NAG-NAG.4: 4 residues within 4Å: Chain A: E.93, N.229, T.231, G.232 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.93 NAG-NAG.5: 4 residues within 4Å: Chain A: Q.288, N.290, N.326, N.404 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.404 NAG-NAG.6: 2 residues within 4Å: Chain A: N.296, I.317 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 7 residues within 4Å: Chain A: N.290, T.292, H.324, N.326, S.406, T.408, R.437 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain A: T.366, T.367, N.380, S.382 Ligands: NAG-NAG.9 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain A: S.382, N.386 Ligands: NAG-NAG.8, NAG-NAG.8 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain A: N.257, N.441 Ligands: NAG-NAG-BMA-MAN-MAN.11 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain B: V.175, R.187, N.192 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 6 residues within 4Å: Chain B: N.290, T.292, H.324, N.326, T.408, R.437 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain B: T.366, T.367, N.380 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain B: Q.357, S.382, N.386 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain B: V.439, S.440, N.441 Ligands: NAG-NAG-BMA-MAN.13 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 5 residues within 4Å: Chain B: N.134, V.135, T.136, N.149, Y.166 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.166 Hydrogen bonds: B:Y.166 NAG-NAG.20: 3 residues within 4Å: Chain D: V.175, R.187, N.192 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.175 NAG-NAG.22: 3 residues within 4Å: Chain D: N.296, I.317, V.435 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 5 residues within 4Å: Chain D: N.290, T.292, H.324, N.326, T.408 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain D: T.366, T.367, N.380, S.382 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 2 residues within 4Å: Chain D: S.382, N.386 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 4 residues within 4Å: Chain D: N.257, P.286, N.441 Ligands: NAG-NAG-BMA-MAN-MAN.21 No protein-ligand interaction detected (PLIP)

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.11: 10 residues within 4Å: Chain A: E.206, V.249, L.256, N.257, N.371, C.372, G.373, V.439, S.440 Ligands: NAG-NAG.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.373 NAG-NAG-BMA-MAN-MAN.21: 7 residues within 4Å: Chain D: P.207, V.249, L.256, N.257, V.439, S.440 Ligands: NAG-NAG.26 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.27: 12 residues within 4Å: Chain D: T.129, Q.131, S.151, F.152, N.153 Chain G: Y.80, N.81, Y.82 Chain H: D.124, R.126, Y.131, Y.139 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:D.124

1 x NAG- NAG- BMA- MAN: 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.13: 7 residues within 4Å: Chain B: P.207, V.249, L.256, N.257, V.439, S.440 Ligands: NAG-NAG.17 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN: 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.18: 11 residues within 4Å: Chain B: Q.131, N.153, R.162, R.181 Chain G: Y.99, E.100, N.103, S.106 Chain H: D.124, Y.125, Y.141 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:Y.125 Hydrogen bonds: G:S.106

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.28: 13 residues within 4Å: Chain D: V.135, T.136, N.149, Y.166, D.315 Chain H: Y.73, D.74, R.92, D.93, N.94, S.95, F.134, W.135 4 PLIP interactions: 2 interactions with chain H, 2 interactions with chain D Hydrophobic interactions: H:F.134, H:W.135, D:Y.166 Hydrogen bonds: D:Y.166

28 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: 2 residues within 4Å: Chain A: T.136, N.138 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain A: R.344, F.347, G.348, N.349 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain A: N.271, I.272, T.273, N.274 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: N.134, R.144, G.145 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain B: T.133, N.134, R.144, K.148 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain B: Q.288, N.290, N.326 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain B: N.349 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: N.271, T.273 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain B: K.227, F.228, N.229, T.231 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: N.296, I.317, V.435 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain B: E.88, N.89 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.100, S.101 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain C: N.107, S.109, E.110 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain C: K.122, E.123, S.125, N.126, Y.127 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain D: N.134, K.148 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain D: N.271, T.273 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain D: Q.288, N.290, N.326 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain D: N.349 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain D: S.453, T.454, N.455 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain D: N.89 Chain E: S.17 Ligand excluded by PLIP NAG.50: 7 residues within 4Å: Chain D: D.225, K.227, F.228, N.229, G.230, T.231, R.268 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain E: N.100, S.101, S.102 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain E: N.107, S.109, E.110 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain E: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain F: N.100, S.102 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain F: N.107, E.110 Ligand excluded by PLIP NAG.56: 5 residues within 4Å: Chain F: E.123, I.124, S.125, 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 gp120: ABD
HIV Envelope ApexGT3 gp41: CEF
PG9.iGL Fab Light Chain: G
PG9.iGL Fab Heavy Chain: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

D
E

C
D

E
F

F
B

G
L

H
H

HIV Envelope ApexGT3 gp120

HIV Envelope ApexGT3 gp41

PG9.iGL Fab Light Chain

PG9.iGL Fab Heavy Chain

Related Entries With Identical Sequence