SMTL ID : 7t74.1

HIV-1 Envelope ApexGT2 in complex with PCT64.35S Fab and RM20A3 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-1-1-mer

Ligands

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.1: 23 residues within 4Å: Chain A: T.129, Q.131, S.151, N.153, R.162 Chain E: D.32, Y.37, L.47, Y.50, G.51, R.54, R.90, Y.92 Chain F: W.33, R.52, M.99, T.100, G.101, E.103, Y.116, L.120, D.122 Chain K: N.160 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:G.51, E:R.54, F:E.103

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.2: 6 residues within 4Å: Chain A: Q.355, T.364, T.365, N.378, S.380 Ligands: NAG.27 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 5 residues within 4Å: Chain A: N.288, T.290, H.322, N.324, T.406 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 6 residues within 4Å: Chain G: Q.355, T.364, T.365, N.378, S.380 Ligands: NAG.41 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain G: N.288, T.290, H.322, N.324 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain G: V.135, T.136, N.149, S.151, Y.166, D.313 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:Y.166 Hydrogen bonds: G:Y.166 NAG-NAG.15: 4 residues within 4Å: Chain G: N.160 Chain K: T.129, Q.131, N.153 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 6 residues within 4Å: Chain K: Q.355, T.364, T.365, N.378, S.380 Ligands: NAG.55 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 5 residues within 4Å: Chain K: N.288, T.290, H.322, N.324, T.406 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 5 residues within 4Å: Chain K: V.135, T.136, N.149, Y.166, D.313 2 PLIP interactions: 2 interactions with chain K Hydrophobic interactions: K:Y.166 Hydrogen bonds: K:Y.166

4 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.4: 9 residues within 4Å: Chain A: S.202, P.205, L.254, N.255, N.369, G.371, V.437, S.438 Ligands: NAG.30 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.5: 10 residues within 4Å: Chain A: V.135, T.136, N.149, Y.166, D.313 Chain F: M.51, T.54, T.55, G.57, G.58 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain A Hydrogen bonds: F:T.54, F:T.55, A:Y.166 NAG-NAG-BMA-MAN.11: 10 residues within 4Å: Chain G: S.202, P.205, V.247, L.254, N.255, N.369, G.371, V.437, S.438 Ligands: NAG.44 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:S.202, G:S.202 NAG-NAG-BMA-MAN.18: 8 residues within 4Å: Chain K: E.204, P.205, L.254, N.255, N.369, 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.6: 4 residues within 4Å: Chain B: N.107, E.110 Chain C: S.107 Ligands: NAG.34 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.110 NAG-FUC.7: 4 residues within 4Å: Chain B: N.100, S.102, W.103, I.130 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.100, B:S.102, B:S.102 Hydrophobic interactions: B:I.130 NAG-FUC.13: 4 residues within 4Å: Chain H: N.107, S.109, E.110 Chain I: S.107 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:S.109, H:S.109 NAG-FUC.14: 4 residues within 4Å: Chain H: N.100, S.102, Y.127, I.130 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:S.102 Hydrophobic interactions: H:Y.127 NAG-FUC.20: 4 residues within 4Å: Chain L: N.107, S.109, E.110 Chain M: S.107 No protein-ligand interaction detected (PLIP) NAG-FUC.21: 5 residues within 4Å: Chain L: N.100, S.102, W.103, Y.127, I.130 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:N.100, L:S.102, L:W.103

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.8: 6 residues within 4Å: Chain F: D.106, Y.119 Chain G: Q.131, S.151, N.153, R.162 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:Y.119, F:Y.119, F:D.106

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

NAG.22: 4 residues within 4Å: Chain A: E.88, N.89 Chain B: G.16, S.17 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: N.227, T.229, S.267, H.344 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.138 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain A: N.347 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: N.269, T.271, N.272 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain A: Q.355, S.380, N.384 Ligands: NAG-NAG.2 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain A: K.327, N.331, W.387 Ligand excluded by PLIP NAG.29: 6 residues within 4Å: Chain A: Q.286, N.288, N.324, V.325, S.326, R.435 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain A: N.255, P.284, N.439 Ligands: NAG-NAG-BMA-MAN.4 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: N.294, I.315, V.433 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain A: V.175, R.185, N.190, T.191 Chain K: R.301 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: N.134, G.145, K.148 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain B: N.114, M.115, Q.119 Ligands: NAG-FUC.6 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: E.123, N.126 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain G: E.88, N.89 Chain H: S.17 Ligand excluded by PLIP NAG.37: 5 residues within 4Å: Chain G: N.227, T.229, S.267, I.270, H.344 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain G: N.138 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain G: N.347 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain G: N.269, T.271, N.272 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain G: Q.355, S.380, N.384 Ligands: NAG-NAG.9 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain G: K.327, N.331, W.387 Ligand excluded by PLIP NAG.43: 6 residues within 4Å: Chain G: Q.286, N.288, N.324, V.325, S.326, R.435 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain G: N.255, P.284, N.439 Ligands: NAG-NAG-BMA-MAN.11 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain G: N.294, I.315, V.433 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain A: R.301 Chain G: R.185, N.190 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain G: N.134, G.145 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain H: D.113, N.114 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain H: E.123, N.126 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain K: E.88, N.89 Chain L: S.17 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain K: N.227, T.229, S.267, H.344 Ligand excluded by PLIP NAG.52: 1 residues within 4Å: Chain K: N.138 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain K: N.347 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain K: N.269, T.271, N.272 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain K: S.380, N.384 Ligands: NAG-NAG.16 Ligand excluded by PLIP NAG.56: 1 residues within 4Å: Chain K: N.331 Ligand excluded by PLIP NAG.57: 6 residues within 4Å: Chain K: Q.286, N.288, N.324, V.325, S.326, R.435 Ligand excluded by PLIP NAG.58: 4 residues within 4Å: Chain K: N.255, P.284, N.439 Ligands: NAG-NAG-BMA-MAN.18 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain K: N.294, I.315, V.433 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain G: R.301 Chain K: R.185, N.190 Ligand excluded by PLIP NAG.61: 3 residues within 4Å: Chain K: N.134, G.145, K.148 Ligand excluded by PLIP NAG.62: 3 residues within 4Å: Chain L: S.109, D.113, N.114 Ligand excluded by PLIP NAG.63: 4 residues within 4Å: Chain L: K.122, E.123, S.125, N.126 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: AGK
HIV Envelope ApexGT2 gp41: BHL
RM20A3 Fab Heavy Chain: CIM
RM20A3 Fab Light Chain: DJN
PCT64.35S Fab Light Chain: E
PCT64.35S Fab Heavy Chain: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

G
C

K
E

B
B

H
D

L
F

C
K

I
M

M
I

D
G

J
N

N
J

E
L

F
H

HIV Envelope ApexGT2 gp120

HIV Envelope ApexGT2 gp41

RM20A3 Fab Heavy Chain

RM20A3 Fab Light Chain

PCT64.35S Fab Light Chain

PCT64.35S Fab Heavy Chain

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