SMTL ID : 7l88.1

BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-3 from animal Rh.32034 (Wk26 time point)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

26 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 A: N.130, G.141, R.167 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain A: V.131, N.133, N.145, Y.162, L.164, D.317 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.162 NAG-NAG.3: 4 residues within 4Å: Chain A: R.189, N.194, T.195 Chain E: R.305 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain A: 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 A: N.273, T.275, N.276 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain A: Q.290, N.292, N.328, S.330, R.439 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain A: N.292, T.294, H.326, N.328, R.439 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 7 residues within 4Å: Chain A: Q.359, T.368, T.369, N.382, S.384, R.414 Ligands: NAG-NAG.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.359 NAG-NAG.10: 3 residues within 4Å: Chain A: S.384, N.388 Ligands: NAG-NAG.9 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain A: E.84, N.85 Chain B: S.10 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 2 residues within 4Å: Chain C: N.130, R.167 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 6 residues within 4Å: Chain C: V.131, N.133, N.145, Y.162, L.164, D.317 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.162 NAG-NAG.14: 4 residues within 4Å: Chain A: R.305 Chain C: R.189, N.194, T.195 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 7 residues within 4Å: Chain C: N.231, T.233, G.234, P.235, I.269, S.271, H.348 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain C: N.273, T.275, N.276 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 5 residues within 4Å: Chain C: N.292, T.294, H.326, N.328, S.408 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 5 residues within 4Å: Chain C: T.368, T.369, N.382, S.384 Ligands: NAG-NAG.20 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain C: Q.359, N.388 Ligands: NAG-NAG.19 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain C: E.84, N.85 Chain D: S.10 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 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.23: 4 residues within 4Å: Chain C: R.305 Chain E: R.189, N.194, T.195 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 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.26: 3 residues within 4Å: Chain E: N.273, T.275, N.276 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 6 residues within 4Å: Chain E: Q.290, N.292, N.328, S.330, N.406, R.439 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:N.406, E:N.406 NAG-NAG.28: 6 residues within 4Å: Chain E: N.292, T.294, H.326, N.328, S.408, R.439 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 5 residues within 4Å: Chain E: T.369, N.382, S.384, R.414 Ligands: NAG.51 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.5: 10 residues within 4Å: Chain A: S.206, E.208, P.209, L.258, N.259, N.373, G.375, V.441, S.442 Ligands: NAG.33 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.375 NAG-NAG-BMA-MAN-MAN.25: 10 residues within 4Å: Chain E: S.206, E.208, P.209, V.251, N.259, N.373, G.375, V.441, S.442 Ligands: NAG.52 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:G.375, E:V.441

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.16: 10 residues within 4Å: Chain C: S.206, E.208, P.209, V.251, L.258, N.259, C.440, V.441, S.442 Ligands: NAG.41 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.441

27 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.30: 4 residues within 4Å: Chain A: Q.127, S.147, F.148, N.149 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: N.298, I.319, V.437 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: N.335, W.391 Ligand excluded by PLIP NAG.33: 5 residues within 4Å: Chain A: P.288, V.441, S.442, N.443 Ligands: NAG-NAG-BMA-MAN-MAN.5 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain A: N.351 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain B: N.93, S.95 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.119, Y.120 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain C: S.147, F.148, N.149 Ligand excluded by PLIP NAG.38: 6 residues within 4Å: Chain C: Q.290, N.292, N.328, V.329, S.330, R.439 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.298, I.319 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.335, W.391 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain C: N.259, P.288, N.443 Ligands: NAG-NAG-BMA-MAN.16 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.133, N.134 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain C: N.351 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain D: N.93, S.95 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain D: N.100 Chain H: X.51 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain D: K.115, E.116, N.119 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain E: N.130, T.132, R.140 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain E: S.147, F.148, N.149 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain E: N.298, I.319, V.437 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain E: N.335, W.391 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain E: Q.359, N.388 Ligands: NAG-NAG.29, NAG-NAG.29 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain E: N.259, P.288, N.443 Ligands: NAG-NAG-BMA-MAN-MAN.25 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain E: E.84, N.85 Chain F: S.10 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain E: N.134, D.321 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain F: N.93, S.95 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain F: K.115, E.116, N.119 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

BG505 SOSIP MD39 - gp120: ACE
BG505 SOSIP MD39 - gp41: BDF
Rh.32034 pAbC-3 - Heavy Chain: G
Rh.32034 pAbC-3 - Light Chain: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

C
A

E
C

B
F

D
B

F
E

G
H

H
L

BG505 SOSIP MD39 - gp120

BG505 SOSIP MD39 - gp41

Rh.32034 pAbC-3 - Heavy Chain

Rh.32034 pAbC-3 - Light Chain

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