SMTL ID : 7l89.1

BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-4 from animal Rh.32034 (Wk26 time point)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-3-3-mer

Ligands

34 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 C: V.131, N.133, N.145, Y.162, L.164, D.317 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 5 residues within 4Å: Chain C: V.171, R.189, N.194, T.195 Chain G: R.305 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.171 NAG-NAG.3: 6 residues within 4Å: Chain C: N.231, T.233, G.234, S.271, H.348 Ligands: NAG-NAG.5 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: N.273, T.275, N.276 Ligands: NAG-NAG.3 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain C: Q.290, N.292, N.328, V.329, S.330, R.439 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain C: N.298, I.319, V.437 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain C: N.292, T.294, H.326, N.328, S.408 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 6 residues within 4Å: Chain C: Q.359, T.368, T.369, N.382, S.384 Ligands: NAG-NAG.10 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.359 NAG-NAG.10: 2 residues within 4Å: Chain C: N.388 Ligands: NAG-NAG.9 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 5 residues within 4Å: Chain C: P.288, V.441, S.442, N.443 Ligands: NAG-NAG-BMA-MAN-MAN.4 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain C: E.84, N.85 Chain D: S.10 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain D: N.93, S.95 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 6 residues within 4Å: Chain E: V.131, N.133, N.145, Y.162, L.164, D.317 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.162 NAG-NAG.15: 4 residues within 4Å: Chain C: R.305 Chain E: R.189, N.194, T.195 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 6 residues within 4Å: Chain E: N.231, T.233, G.234, P.235, S.271, H.348 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain E: N.273, T.275, N.276 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain E: Q.290, N.292, N.328, R.439 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 5 residues within 4Å: Chain E: N.292, T.294, H.326, N.328, R.439 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 6 residues within 4Å: Chain E: Q.359, T.368, T.369, N.382, S.384 Ligands: NAG-NAG.22 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:Q.359 NAG-NAG.22: 3 residues within 4Å: Chain E: Q.359, N.388 Ligands: NAG-NAG.21 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain E: P.288, V.441, N.443 Ligands: NAG-NAG-BMA-MAN-MAN.17 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain E: E.84, N.85 Chain F: G.6, S.10 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 2 residues within 4Å: Chain F: N.93, S.95 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain F: N.100, S.102, E.103 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 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.28: 2 residues within 4Å: Chain G: Q.127, N.149 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 5 residues within 4Å: Chain E: R.305 Chain G: V.171, R.189, N.194, T.195 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 3 residues within 4Å: Chain G: N.273, T.275, N.276 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 5 residues within 4Å: Chain G: Q.290, N.292, N.328, N.406, R.439 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.406 NAG-NAG.33: 3 residues within 4Å: Chain G: N.298, I.319, V.437 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 5 residues within 4Å: Chain G: N.292, T.294, H.326, N.328, S.408 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 6 residues within 4Å: Chain G: Q.359, T.368, T.369, N.382, S.384 Ligands: NAG-NAG.36 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 2 residues within 4Å: Chain G: N.388 Ligands: NAG-NAG.35 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 5 residues within 4Å: Chain G: P.288, V.441, S.442, N.443 Ligands: NAG-NAG-BMA-MAN-MAN.30 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.4: 10 residues within 4Å: Chain C: S.206, E.208, V.251, L.258, N.259, N.373, G.375, V.441, S.442 Ligands: NAG-NAG.11 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.17: 11 residues within 4Å: Chain E: H.63, S.206, E.208, V.251, L.258, N.259, N.373, G.375, V.441, S.442 Ligands: NAG-NAG.23 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:G.375, E:V.441 NAG-NAG-BMA-MAN-MAN.30: 10 residues within 4Å: Chain G: S.206, E.208, P.209, V.251, L.258, N.259, G.375, V.441, S.442 Ligands: NAG-NAG.37 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:V.441

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

NAG.38: 2 residues within 4Å: Chain C: N.130, R.167 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain C: Q.127, S.147, F.148, N.149 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.335, W.391 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: N.133, N.134, G.320 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain D: N.119 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain E: N.130 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain E: S.147, F.148, N.149 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain E: N.298, I.319, V.437 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain E: N.335 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain E: N.134 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain F: N.119 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain G: N.130, K.144, R.167 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain G: N.231, T.233, S.271, H.348 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain G: E.84, N.85 Chain H: S.10 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain G: N.133, N.134, G.320 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain H: N.93, S.95 Ligand excluded by PLIP NAG.54: 5 residues within 4Å: Chain H: K.115, E.116, S.118, N.119, Y.120 Ligand excluded by PLIP

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-4 - Heavy Chain: A
Rh.32034 pAbC-4 - 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
E

E
A

G
B

D
F

F
C

H
D

Rh.32034 pAbC-4 - Heavy Chain

Rh.32034 pAbC-4 - Light Chain

BG505 SOSIP MD39 - gp120

BG505 SOSIP MD39 - gp41

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