SMTL ID : 7l8b.1

BG505 SOSIP MD39 in complex with the polyclonal Fab pAbC-2 from animal Rh.33104 (Wk26 time point)

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

25 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: 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.2: 4 residues within 4Å: Chain A: R.160, N.165, T.166 Chain E: R.276 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 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.5: 3 residues within 4Å: Chain A: N.269, I.290, Q.406 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain A: N.263, T.265, H.297, N.299 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 6 residues within 4Å: Chain A: Q.330, T.339, T.340, N.353, S.355 Ligands: NAG.34 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.330 NAG-NAG.8: 4 residues within 4Å: Chain A: N.230, P.259, N.414 Ligands: NAG-NAG-BMA-MAN-MAN.3 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: N.101, R.111, G.112 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.111 NAG-NAG.10: 6 residues within 4Å: Chain C: V.102, N.104, N.116, Y.133, L.135, D.288 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.133 NAG-NAG.11: 4 residues within 4Å: Chain A: R.276 Chain C: V.142, R.160, N.165 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:V.142 NAG-NAG.12: 5 residues within 4Å: Chain C: N.202, T.204, P.206, S.242, H.319 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 3 residues within 4Å: Chain C: N.244, T.246, N.247 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 5 residues within 4Å: Chain C: Q.261, N.263, N.299, S.301, R.410 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 5 residues within 4Å: Chain C: N.263, T.265, H.297, N.299, R.410 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain C: Q.330, T.339, T.340, N.353 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 1 residues within 4Å: Chain C: N.359 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain C: E.55, N.56 Chain D: S.11 Chain H: X.62 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 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 NAG-NAG.21: 4 residues within 4Å: Chain C: R.276 Chain E: R.160, N.165, T.166 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 6 residues within 4Å: Chain E: N.202, T.204, P.206, I.240, S.242, H.319 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain E: N.244, T.246, N.247 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 5 residues within 4Å: Chain E: Q.261, N.263, N.299, S.301, R.410 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 4 residues within 4Å: Chain E: N.263, H.297, N.299, R.410 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 5 residues within 4Å: Chain E: Q.330, T.339, T.340, N.353, S.355 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 4 residues within 4Å: Chain E: P.259, V.412, N.414 Ligands: NAG-NAG-BMA-MAN-MAN.23 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.3: 8 residues within 4Å: Chain A: P.180, L.229, N.230, N.344, G.346, V.412, S.413 Ligands: NAG-NAG.8 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.13: 7 residues within 4Å: Chain C: E.179, L.229, N.230, G.346, V.412, S.413 Ligands: NAG.43 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.23: 9 residues within 4Å: Chain E: S.177, E.179, L.229, N.230, N.344, G.346, V.412, S.413 Ligands: NAG-NAG.28 No protein-ligand interaction detected (PLIP)

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

NAG.29: 2 residues within 4Å: Chain A: N.101, G.112 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain A: S.118, F.119, N.120 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: N.202, T.204, S.242 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain A: Q.261, N.263, N.299, V.300, S.301 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain A: N.306, W.362 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: N.359 Ligands: NAG-NAG.7 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: E.55, N.56 Chain B: S.11 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain A: N.104, N.105 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain B: N.94, S.96 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain B: N.101, S.103, E.104 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain B: N.120 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: S.118, F.119, N.120 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain C: N.269, I.290, V.408 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.306, W.362 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain C: N.230, N.414 Ligands: NAG-NAG-BMA-MAN-MAN.13 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: N.105, D.292 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain D: N.94, S.96 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain D: N.101 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain D: K.116, E.117, N.120 Ligand excluded by PLIP NAG.48: 5 residues within 4Å: Chain E: C.99, T.100, N.101, K.115, Y.159 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain E: Q.98, S.118, F.119, N.120 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain E: N.269, I.290, V.408 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain E: N.306 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain E: G.356, N.359 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain E: E.55, N.56 Chain F: S.11 Ligand excluded by PLIP NAG.54: 3 residues within 4Å: Chain E: N.104, N.105, D.292 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain F: N.94, S.96, W.97 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain F: N.101, S.103 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain F: K.116, E.117, N.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

BG505 SOSIP MD39 - gp120: ACE
BG505 SOSIP MD39 - gp41: BDF
Rh.33104 pAbC-2 - Heavy Chain: G
Rh.33104 pAbC-2 - Light Chain: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
A

E
E

B
D

D
B

F
F

G
H

H
L

BG505 SOSIP MD39 - gp120

BG505 SOSIP MD39 - gp41

Rh.33104 pAbC-2 - Heavy Chain

Rh.33104 pAbC-2 - Light Chain

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