SMTL ID : 7l8a.1

BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-1 from animal Rh.33104 (Wk26 time point)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-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 A: V.102, N.104, N.116, L.135, D.288 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain A: R.160, N.165, T.166 Chain G: R.276 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: N.202, T.204, P.206, S.242, I.245, H.319 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.244, T.246, N.247 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.246 NAG-NAG.6: 4 residues within 4Å: Chain A: Q.261, N.263, N.299, R.410 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: N.269, I.290, V.408 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain A: N.263, T.265, H.297, N.299, S.379 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 6 residues within 4Å: Chain A: Q.330, T.339, T.340, N.353, S.355 Ligands: NAG.36 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain A: N.230, P.259, N.414 Ligands: NAG-NAG-BMA-MAN.4 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain A: E.55, N.56 Chain B: S.10 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain E: V.102, N.104, N.116, L.135, D.288 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain A: R.276 Chain E: R.160, N.165 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain E: N.202, G.203, T.204, H.319 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 3 residues within 4Å: Chain E: N.244, T.246, N.247 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 6 residues within 4Å: Chain E: Q.261, N.263, N.299, V.300, S.301, R.410 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 6 residues within 4Å: Chain E: N.263, T.265, H.297, N.299, S.379, T.381 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 5 residues within 4Å: Chain E: Q.330, T.339, T.340, N.353 Ligands: NAG-NAG.20 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 3 residues within 4Å: Chain E: Q.330, N.359 Ligands: NAG-NAG.19 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain E: P.259, V.412, N.414 Ligands: NAG-NAG-BMA-MAN-MAN.15 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 2 residues within 4Å: Chain E: E.55, N.56 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain G: V.102, N.116, Y.133, L.135 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:Y.133 NAG-NAG.24: 5 residues within 4Å: Chain E: R.276 Chain G: V.142, R.160, N.165, T.166 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 6 residues within 4Å: Chain G: N.202, T.204, P.206, S.242, I.245, H.319 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 3 residues within 4Å: Chain G: N.244, T.246, N.247 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 2 residues within 4Å: Chain G: N.269, V.408 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 5 residues within 4Å: Chain G: N.263, T.265, H.297, N.299, R.410 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 7 residues within 4Å: Chain G: Q.330, T.339, T.340, N.353, S.355, R.385 Ligands: NAG-NAG.31 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 3 residues within 4Å: Chain G: Q.330, N.359 Ligands: NAG-NAG.30 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 4 residues within 4Å: Chain G: N.230, P.259, N.414 Ligands: NAG-NAG-BMA-MAN-MAN.26 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 3 residues within 4Å: Chain G: E.55, N.56 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.4: 9 residues within 4Å: Chain A: S.177, E.179, L.229, N.230, N.344, G.346, V.412, S.413 Ligands: NAG-NAG.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.346, A:S.177

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.15: 9 residues within 4Å: Chain E: E.179, V.222, L.229, N.230, N.344, G.346, V.412, S.413 Ligands: NAG-NAG.21 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:V.412 NAG-NAG-BMA-MAN-MAN.26: 9 residues within 4Å: Chain G: S.177, E.179, L.229, N.230, N.344, G.346, V.412, S.413 Ligands: NAG-NAG.32 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:G.346, G:V.412

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

NAG.34: 2 residues within 4Å: Chain A: N.101, R.138 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain A: Q.98, S.118, F.119, N.120 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain A: Q.330, N.359 Ligands: NAG-NAG.9 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain A: N.104, N.105, D.292 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain A: N.306 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain B: N.93, S.95 Ligand excluded by PLIP NAG.40: 1 residues within 4Å: Chain B: N.119 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain E: N.101, R.111, G.112 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain E: S.118, F.119, N.120 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain E: N.269, I.290, V.408 Ligand excluded by PLIP NAG.44: 5 residues within 4Å: Chain E: K.302, N.306, T.366, S.367, V.368 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain E: N.105, G.291, D.292 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain E: N.322 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain D: X.58 Chain E: N.365 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain F: W.92, N.93 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain F: N.119 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain G: N.101, G.112, R.138 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain G: Q.98, S.118, F.119, N.120 Ligand excluded by PLIP NAG.52: 5 residues within 4Å: Chain G: Q.261, N.263, N.299, S.301, R.410 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain G: N.306 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain G: N.105, D.292 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain H: W.92, N.93, S.95 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain H: 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: AEG
BG505 SOSIP MD39 - gp41: BFH
Rh.33104 pAbC-1 - Heavy Chain: C
Rh.33104 pAbC-1 - Light Chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

E
A

G
C

B
F

F
B

H
D

C
H

D
L

BG505 SOSIP MD39 - gp120

BG505 SOSIP MD39 - gp41

Rh.33104 pAbC-1 - Heavy Chain

Rh.33104 pAbC-1 - Light Chain

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