SMTL ID : 7l86.1

BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-1 from animal Rh.32034 (Wk26 time point)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-3-3-mer

Ligands

30 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: 5 residues within 4Å: Chain C: N.133, N.145, S.147, Y.162, D.317 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.162 NAG-NAG.2: 4 residues within 4Å: Chain C: R.189, I.191, N.194, T.195 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.191 NAG-NAG.3: 5 residues within 4Å: Chain C: N.231, T.233, I.269, S.271, H.348 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 2 residues within 4Å: Chain C: N.273, N.276 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 7 residues within 4Å: Chain C: Q.290, N.292, N.328, V.329, S.330, R.439 Ligands: NAG-NAG.8 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.406 NAG-NAG.7: 2 residues within 4Å: Chain C: N.298, I.319 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain C: N.292, T.294, H.326, N.328, S.408 Ligands: NAG-NAG.6 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: 3 residues within 4Å: Chain C: Q.359, N.388 Ligands: NAG-NAG.9 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 6 residues within 4Å: Chain E: V.131, N.133, N.145, Y.162, L.164, D.317 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain E: R.189, N.194, T.195 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain E: N.231, T.233, P.235, S.271, H.348 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain E: N.273, T.275, N.276 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain E: Q.290, N.292, N.328 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain E: N.298, I.319 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 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.19: 5 residues within 4Å: Chain E: Q.359, T.368, T.369, N.382 Ligands: NAG-NAG.20 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain E: Q.359, S.384, N.388 Ligands: NAG-NAG.19 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain G: V.131, N.145, Y.162, D.317 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: Chain E: R.305 Chain G: R.189, N.194, T.195 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain G: N.231, T.233, S.271, H.348 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 3 residues within 4Å: Chain G: N.273, T.275, N.276 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 5 residues within 4Å: Chain G: Q.290, N.292, N.328, S.330, R.439 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 4 residues within 4Å: Chain G: N.292, T.294, H.326, N.328 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 6 residues within 4Å: Chain G: Q.359, T.368, T.369, N.382, S.384 Ligands: NAG-NAG.29 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 3 residues within 4Å: Chain G: Q.359, N.388 Ligands: NAG-NAG.28 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 4 residues within 4Å: Chain G: P.288, V.441, N.443 Ligands: NAG-NAG-BMA-MAN-MAN.24 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 3 residues within 4Å: Chain G: E.84, N.85 Chain H: S.10 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 7 residues within 4Å: Chain A: X.102, X.103, X.104, X.105 Chain G: G.453, G.454, N.457 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 2 residues within 4Å: Chain B: X.93 Chain G: N.351 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: 8 residues within 4Å: Chain C: S.206, E.208, V.251, L.258, N.259, V.441, S.442 Ligands: NAG.37 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.441 NAG-NAG-BMA-MAN-MAN.14: 9 residues within 4Å: Chain E: H.63, E.208, L.258, N.259, N.373, G.375, V.441, S.442 Ligands: NAG.45 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:V.441 NAG-NAG-BMA-MAN-MAN.24: 8 residues within 4Å: Chain G: S.206, E.208, L.258, N.259, G.375, V.441, S.442 Ligands: NAG-NAG.30 No protein-ligand interaction detected (PLIP)

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

NAG.34: 2 residues within 4Å: Chain C: N.130, K.144 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain C: Q.127, S.147, F.148, N.149 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain C: K.331, N.335, W.391 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain C: V.441, S.442, N.443 Ligands: NAG-NAG-BMA-MAN-MAN.4 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain C: E.84, N.85 Chain D: S.10 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain C: N.351 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain D: N.93, S.95 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain D: N.119 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain E: N.130, T.132, K.144 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain E: S.147, F.148, N.149 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain E: N.335, T.390, W.391 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain E: V.441, S.442, N.443 Ligands: NAG-NAG-BMA-MAN-MAN.14 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain E: E.84, N.85 Chain F: S.10 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain E: N.133, N.134, D.321 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain E: N.351 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain F: N.93, S.95 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain F: E.116, N.119, Y.120 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain G: N.130 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain G: S.147, F.148, N.149 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain G: N.298, I.319, V.437 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain G: N.335 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain G: N.134 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain H: N.93, S.95 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain H: 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

Rh.32034 pAbC-1 - Heavy Chain: A
Rh.32034 pAbC-1 - 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
C

G
A

D
F

F
D

H
B

Rh.32034 pAbC-1 - Heavy Chain

Rh.32034 pAbC-1 - Light Chain

BG505 SOSIP MD39 - gp120

BG505 SOSIP MD39 - gp41

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