SMTL ID : 7t75.1 (2 other biounits)

HIV-1 Envelope ApexGT2 in complex with RM20A3 Fab

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

9 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: Q.355, T.364, T.365, N.378, S.380 Ligands: NAG.13 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain A: N.288, T.290, H.322, N.324, S.404, T.406 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain A: T.136, N.149, Y.166, L.168, G.312, D.313 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.166 Hydrogen bonds: A:Y.166 NAG-NAG.22: 6 residues within 4Å: Chain E: Q.355, T.364, T.365, N.378, S.380 Ligands: NAG.34 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 6 residues within 4Å: Chain E: N.288, T.290, H.322, N.324, S.404, T.406 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 6 residues within 4Å: Chain E: T.136, N.149, Y.166, L.168, G.312, D.313 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:Y.166 Hydrogen bonds: E:Y.166 NAG-NAG.43: 6 residues within 4Å: Chain I: Q.355, T.364, T.365, N.378, S.380 Ligands: NAG.55 No protein-ligand interaction detected (PLIP) NAG-NAG.44: 6 residues within 4Å: Chain I: N.288, T.290, H.322, N.324, S.404, T.406 No protein-ligand interaction detected (PLIP) NAG-NAG.46: 6 residues within 4Å: Chain I: T.136, N.149, Y.166, L.168, G.312, D.313 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:Y.166 Hydrogen bonds: I:Y.166

3 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.3: 8 residues within 4Å: Chain A: P.205, L.254, N.255, N.369, G.371, V.437, S.438 Ligands: NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.24: 8 residues within 4Å: Chain E: P.205, L.254, N.255, N.369, G.371, V.437, S.438 Ligands: NAG.37 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.45: 8 residues within 4Å: Chain I: P.205, L.254, N.255, N.369, G.371, V.437, S.438 Ligands: NAG.58 No protein-ligand interaction detected (PLIP)

6 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.5: 4 residues within 4Å: Chain B: N.107, E.110 Chain C: S.107 Ligands: NAG.20 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.107, B:E.110 NAG-FUC.6: 4 residues within 4Å: Chain B: N.100, S.102, Y.127, I.130 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.100, B:S.102 Hydrophobic interactions: B:Y.127 NAG-FUC.26: 4 residues within 4Å: Chain F: N.107, E.110 Chain G: S.107 Ligands: NAG.41 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.107, F:E.110 NAG-FUC.27: 4 residues within 4Å: Chain F: N.100, S.102, Y.127, I.130 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.100, F:S.102 Hydrophobic interactions: F:Y.127 NAG-FUC.47: 4 residues within 4Å: Chain J: N.107, E.110 Chain K: S.107 Ligands: NAG.62 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:N.107, J:E.110 NAG-FUC.48: 4 residues within 4Å: Chain J: N.100, S.102, Y.127, I.130 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:N.100, J:S.102 Hydrophobic interactions: J:Y.127

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

NAG.7: 4 residues within 4Å: Chain A: E.88, N.89 Chain B: G.13, S.17 Ligand excluded by PLIP NAG.8: 5 residues within 4Å: Chain A: T.129, Q.131, S.151, F.152, N.153 Ligand excluded by PLIP NAG.9: 6 residues within 4Å: Chain A: N.227, T.229, I.265, S.267, I.270, H.344 Ligand excluded by PLIP NAG.10: 1 residues within 4Å: Chain A: N.138 Ligand excluded by PLIP NAG.11: 1 residues within 4Å: Chain A: N.347 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.269, T.271, N.272 Ligand excluded by PLIP NAG.13: 5 residues within 4Å: Chain A: Q.355, S.380, N.384 Ligands: NAG-NAG.1, NAG-NAG.1 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain A: K.327, N.331, W.387 Ligand excluded by PLIP NAG.15: 6 residues within 4Å: Chain A: Q.286, N.288, N.324, V.325, S.326, R.435 Ligand excluded by PLIP NAG.16: 6 residues within 4Å: Chain A: N.255, P.284, V.437, S.438, N.439 Ligands: NAG-NAG-BMA-MAN.3 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: N.294, I.315, V.433 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: V.175, R.185, N.190, T.191 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain A: N.134, G.145 Ligand excluded by PLIP NAG.20: 5 residues within 4Å: Chain B: S.109, E.110, D.113, N.114 Ligands: NAG-FUC.5 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain B: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain E: E.88, N.89 Chain F: G.13, S.17 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain E: T.129, Q.131, S.151, F.152, N.153 Ligand excluded by PLIP NAG.30: 6 residues within 4Å: Chain E: N.227, T.229, I.265, S.267, I.270, H.344 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain E: N.138 Ligand excluded by PLIP NAG.32: 1 residues within 4Å: Chain E: N.347 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain E: N.269, T.271, N.272 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain E: Q.355, S.380, N.384 Ligands: NAG-NAG.22, NAG-NAG.22 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain E: K.327, N.331, W.387 Ligand excluded by PLIP NAG.36: 6 residues within 4Å: Chain E: Q.286, N.288, N.324, V.325, S.326, R.435 Ligand excluded by PLIP NAG.37: 6 residues within 4Å: Chain E: N.255, P.284, V.437, S.438, N.439 Ligands: NAG-NAG-BMA-MAN.24 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain E: N.294, I.315, V.433 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain E: V.175, R.185, N.190, T.191 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain E: N.134, G.145 Ligand excluded by PLIP NAG.41: 5 residues within 4Å: Chain F: S.109, E.110, D.113, N.114 Ligands: NAG-FUC.26 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain F: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain I: E.88, N.89 Chain J: G.13, S.17 Ligand excluded by PLIP NAG.50: 5 residues within 4Å: Chain I: T.129, Q.131, S.151, F.152, N.153 Ligand excluded by PLIP NAG.51: 6 residues within 4Å: Chain I: N.227, T.229, I.265, S.267, I.270, H.344 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain I: N.138 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain I: N.347 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain I: N.269, T.271, N.272 Ligand excluded by PLIP NAG.55: 5 residues within 4Å: Chain I: Q.355, S.380, N.384 Ligands: NAG-NAG.43, NAG-NAG.43 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain I: K.327, N.331, W.387 Ligand excluded by PLIP NAG.57: 6 residues within 4Å: Chain I: Q.286, N.288, N.324, V.325, S.326, R.435 Ligand excluded by PLIP NAG.58: 6 residues within 4Å: Chain I: N.255, P.284, V.437, S.438, N.439 Ligands: NAG-NAG-BMA-MAN.45 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain I: N.294, I.315, V.433 Ligand excluded by PLIP NAG.60: 4 residues within 4Å: Chain I: V.175, R.185, N.190, T.191 Ligand excluded by PLIP NAG.61: 2 residues within 4Å: Chain I: N.134, G.145 Ligand excluded by PLIP NAG.62: 5 residues within 4Å: Chain J: S.109, E.110, D.113, N.114 Ligands: NAG-FUC.47 Ligand excluded by PLIP NAG.63: 3 residues within 4Å: Chain J: 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 ApexGT2 gp120: AEI
HIV Envelope ApexGT2 gp41: BFJ
RM20A3 Fab Heavy Chain: CGK
RM20A3 Fab Light Chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
A

B
B

F
B

J
B

C
H

G
H

K
H

D
L

H
L

L
L

HIV Envelope ApexGT2 gp120

HIV Envelope ApexGT2 gp41

RM20A3 Fab Heavy Chain

RM20A3 Fab Light Chain

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