SMTL ID : 7l87.1

BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-2 from animal Rh.32034 (Wk26 time point)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-3-3-mer

Ligands

33 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: 3 residues within 4Å: Chain C: N.130, G.141, R.167 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain C: N.145, Y.162, L.164, D.317 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.162 NAG-NAG.3: 4 residues within 4Å: Chain C: V.171, R.189, N.194, T.195 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain C: N.231, T.233, G.234, P.235, S.271, H.348 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain C: N.273, T.275, N.276 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 6 residues within 4Å: Chain C: Q.290, N.292, N.328, S.330, S.408, R.439 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain C: N.298, I.319, Q.435 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain C: Q.359, S.360, T.368, T.369, N.382 Ligands: NAG-NAG.11 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain C: S.384, N.388 Ligands: NAG-NAG.10 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain C: N.259, P.288, V.441, S.442, N.443 Ligands: NAG-NAG-BMA-MAN.5 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: E.84, N.85 Chain D: S.10 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain E: N.130, R.140 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain E: N.133, N.145, Y.162, D.317 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain E: R.189, N.194, T.195 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 6 residues within 4Å: Chain E: N.231, T.233, G.234, P.235, S.271, H.348 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:P.235 NAG-NAG.19: 3 residues within 4Å: Chain E: N.273, T.275, N.276 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 6 residues within 4Å: Chain E: Q.290, N.292, N.328, V.329, S.330, N.406 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.406, E:N.406 NAG-NAG.21: 2 residues within 4Å: Chain E: N.298, I.319 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 6 residues within 4Å: Chain E: Q.359, T.368, T.369, N.382, S.384 Ligands: NAG-NAG.24 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain E: Q.359, S.384, N.388 Ligands: NAG-NAG.23 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain E: N.259, N.443 Ligands: NAG-NAG-BMA-MAN-MAN.18 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain E: E.84, N.85 Chain F: S.10 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain G: N.130, G.141, R.167 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 6 residues within 4Å: Chain G: V.131, N.133, N.145, Y.162, L.164, D.317 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:Y.162 NAG-NAG.29: 4 residues within 4Å: Chain G: V.171, R.189, N.194, T.195 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 5 residues within 4Å: Chain G: N.231, T.233, G.234, S.271, H.348 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 2 residues within 4Å: Chain G: N.273, T.275 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 6 residues within 4Å: Chain G: Q.290, N.292, N.328, V.329, S.330, R.439 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 2 residues within 4Å: Chain G: N.298, V.437 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 6 residues within 4Å: Chain G: Q.359, T.368, T.369, N.382, S.384 Ligands: NAG-NAG.37 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 3 residues within 4Å: Chain G: Q.359, N.388 Ligands: NAG-NAG.36 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 4 residues within 4Å: Chain G: P.288, V.441, N.443 Ligands: NAG-NAG-BMA-MAN-MAN.31 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 3 residues within 4Å: Chain G: E.84, N.85 Chain H: S.10 No protein-ligand interaction detected (PLIP)

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.5: 6 residues within 4Å: Chain C: V.251, N.259, N.373, V.441, S.442 Ligands: NAG-NAG.12 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.375

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.9: 4 residues within 4Å: Chain C: T.294, H.326, N.328, R.439 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 5 residues within 4Å: Chain E: N.292, T.294, H.326, N.328, S.408 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.35: 6 residues within 4Å: Chain G: N.292, T.294, H.326, N.328, S.408, T.410 No protein-ligand interaction detected (PLIP)

2 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.18: 10 residues within 4Å: Chain E: S.206, E.208, V.251, L.258, N.259, N.373, G.375, V.441, S.442 Ligands: NAG-NAG.25 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.375 NAG-NAG-BMA-MAN-MAN.31: 9 residues within 4Å: Chain G: E.208, L.258, N.259, N.373, G.375, C.440, V.441, S.442 Ligands: NAG-NAG.38 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:V.441

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

NAG.40: 3 residues within 4Å: Chain C: S.147, F.148, N.149 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.149 NAG.41: 2 residues within 4Å: Chain C: N.335, W.391 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.335 NAG.42: 1 residues within 4Å: Chain C: N.351 No protein-ligand interaction detected (PLIP) NAG.43: 2 residues within 4Å: Chain D: N.93, S.95 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.93, D:S.95 NAG.44: 3 residues within 4Å: Chain E: S.147, F.148, N.149 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.149 NAG.45: 3 residues within 4Å: Chain E: K.331, N.335, W.391 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:K.331 NAG.46: 2 residues within 4Å: Chain E: N.134, D.321 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:D.321 NAG.47: 1 residues within 4Å: Chain E: N.351 No protein-ligand interaction detected (PLIP) NAG.48: 3 residues within 4Å: Chain F: P.91, W.92, N.93 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:P.91 NAG.49: 3 residues within 4Å: Chain G: S.147, F.148, N.149 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.149 NAG.50: 2 residues within 4Å: Chain G: N.335, W.391 No protein-ligand interaction detected (PLIP) NAG.51: 2 residues within 4Å: Chain G: N.133, N.134 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.134 NAG.52: 2 residues within 4Å: Chain H: N.93, S.95 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:S.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Antanasijevic, A. et al., Polyclonal antibody responses to HIV Env immunogens resolved using cryoEM. Nat Commun (2021)

Release Date

2021-08-04

Peptides

Rh.32034 pAbC-2 - Heavy Chain: A
Rh.32034 pAbC-2 - Light Chain: B
BG505 SOSIP MD39 - gp120: CEG
BG505 SOSIP MD39 - gp41: DFH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
C

E
A

G
D

D
E

F
B

H
F

Rh.32034 pAbC-2 - Heavy Chain

Rh.32034 pAbC-2 - Light Chain

BG505 SOSIP MD39 - gp120

BG505 SOSIP MD39 - gp41

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