SMTL ID : 7l8c.1

BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-3 from animal Rh.33104 (Wk26 time point)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

36 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: 4 residues within 4Å: Chain A: R.160, N.165, T.166 Chain E: R.276 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.244, T.246, N.247 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain A: N.263, T.265, H.297, N.299, S.379, R.410 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain A: T.339, N.353, S.355 Ligands: NAG-NAG.12 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.230, P.259, N.414 Ligands: NAG-NAG-BMA-MAN-MAN.2 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain A: Q.261, N.263, N.299, S.301, R.410 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain A: E.55, N.56 Chain B: G.7, G.10, S.11 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain A: N.202, T.204, G.205, P.206, S.242, H.319 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain A: N.269, I.290, Q.406 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain A: S.355, N.359 Ligands: NAG-NAG.5 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain B: N.94, S.96 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 2 residues within 4Å: Chain C: N.101, R.138 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain C: N.104, N.116, Y.133, D.288 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.133 NAG-NAG.16: 4 residues within 4Å: Chain A: R.276 Chain C: R.160, N.165, T.166 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain C: N.244, T.246, N.247 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 5 residues within 4Å: Chain C: Q.261, N.263, N.299, S.301, R.410 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 5 residues within 4Å: Chain C: N.263, T.265, H.297, N.299, R.410 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 6 residues within 4Å: Chain C: Q.330, T.339, T.340, N.353, S.355 Ligands: NAG.51 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 5 residues within 4Å: Chain C: L.233, P.259, V.412, N.414 Ligands: NAG-NAG-BMA.17 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 3 residues within 4Å: Chain C: E.55, N.56 Chain D: S.11 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain C: Q.98, S.118, F.119, N.120 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 5 residues within 4Å: Chain C: N.202, T.204, G.205, P.206, S.242 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 3 residues within 4Å: Chain C: N.269, I.290, V.408 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 2 residues within 4Å: Chain D: N.94, S.96 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 2 residues within 4Å: Chain E: N.101, R.138 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 5 residues within 4Å: Chain C: R.276 Chain E: V.142, R.160, N.165, T.166 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 3 residues within 4Å: Chain E: N.244, T.246, N.247 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 5 residues within 4Å: Chain E: Q.261, N.263, N.299, S.301, R.410 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 5 residues within 4Å: Chain E: N.263, T.265, H.297, N.299, R.410 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 5 residues within 4Å: Chain E: T.339, T.340, N.353, S.355 Ligands: NAG-NAG.37 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 3 residues within 4Å: Chain E: S.355, N.359 Ligands: NAG-NAG.36 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 4 residues within 4Å: Chain E: N.230, P.259, N.414 Ligands: NAG-NAG-BMA-MAN-MAN.32 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 3 residues within 4Å: Chain E: E.55, N.56 Chain F: S.11 No protein-ligand interaction detected (PLIP) NAG-NAG.40: 7 residues within 4Å: Chain E: N.202, T.204, G.205, P.206, I.240, S.242, H.319 No protein-ligand interaction detected (PLIP) NAG-NAG.41: 3 residues within 4Å: Chain E: N.269, I.290, V.408 No protein-ligand interaction detected (PLIP) NAG-NAG.42: 2 residues within 4Å: Chain F: N.94, S.96 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.2: 8 residues within 4Å: Chain A: E.179, L.229, N.230, N.344, G.346, V.412, S.413 Ligands: NAG-NAG.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.346 NAG-NAG-BMA-MAN-MAN.32: 8 residues within 4Å: Chain E: E.179, L.229, N.230, N.344, G.346, V.412, S.413 Ligands: NAG-NAG.38 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.346

4 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.7: 6 residues within 4Å: Chain A: V.102, N.104, N.116, Y.133, L.135, D.288 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.133 NAG-NAG-BMA.17: 9 residues within 4Å: Chain C: E.179, V.222, L.229, N.230, N.344, C.411, V.412, S.413 Ligands: NAG-NAG.22 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:V.412 NAG-NAG-BMA.28: 2 residues within 4Å: Chain D: N.101 Chain H: X.50 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 6 residues within 4Å: Chain E: V.102, N.104, N.116, Y.133, L.135, D.288 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.133

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

NAG.43: 3 residues within 4Å: Chain A: S.118, F.119, N.120 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain A: K.302, N.306 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain A: N.104, N.105 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain A: N.101, K.115 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain A: N.322 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain B: N.101, S.103 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain B: E.117, N.120, Y.121 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain C: N.306, W.362 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain C: Q.330, N.359 Ligands: NAG-NAG.21 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain C: N.322, N.323 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain C: N.105 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain D: N.120 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain E: S.118, F.119, N.120 Ligand excluded by PLIP NAG.56: 1 residues within 4Å: Chain E: N.306 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain E: N.104, N.105 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain F: N.101, S.103 Ligand excluded by PLIP NAG.59: 4 residues within 4Å: Chain F: K.116, E.117, N.120, Y.121 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.33104 pAbC-3 - Heavy Chain: G
Rh.33104 pAbC-3 - Light Chain: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
D

B
B

D
E

F
F

G
H

H
L

BG505 SOSIP MD39 - gp120

BG505 SOSIP MD39 - gp41

Rh.33104 pAbC-3 - Heavy Chain

Rh.33104 pAbC-3 - Light Chain

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