SMTL ID : 8tox.1

Cryo-EM structure of BG505 Env mutant A517E in complex with antibody ACS202 Fab

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

33 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: 2 residues within 4Å: Chain A: N.100, S.102 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: E.123, N.126, Y.127 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain B: N.103, G.114, K.117 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain B: R.162, I.164, N.167 Chain D: R.278 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:I.164 NAG-NAG.7: 4 residues within 4Å: Chain B: N.204, T.206, S.244, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 7 residues within 4Å: Chain B: H.55, K.199, N.211 Chain G: G.54, H.55, T.72, N.75 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:T.72 NAG-NAG.11: 3 residues within 4Å: Chain B: Q.263, N.265, T.301 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain B: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 1 residues within 4Å: Chain B: N.324 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 4 residues within 4Å: Chain B: N.355, S.357 Ligands: NAG-NAG-BMA.15, NAG.55 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain B: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.9 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain C: N.100, S.102 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain C: E.123, N.126, Y.127 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain D: N.103, G.114, K.117 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain D: R.162, I.164, N.167 Chain F: R.278 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:I.164 NAG-NAG.24: 4 residues within 4Å: Chain D: N.204, T.206, S.244, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 7 residues within 4Å: Chain D: H.55, K.199, N.211 Chain I: G.54, H.55, T.72, N.75 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:T.72 NAG-NAG.28: 3 residues within 4Å: Chain D: Q.263, N.265, T.301 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 3 residues within 4Å: Chain D: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 1 residues within 4Å: Chain D: N.324 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 4 residues within 4Å: Chain D: N.355, S.357 Ligands: NAG-NAG-BMA.32, NAG.59 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 4 residues within 4Å: Chain D: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.26 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 2 residues within 4Å: Chain E: N.100, S.102 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 3 residues within 4Å: Chain E: E.123, N.126, Y.127 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 3 residues within 4Å: Chain F: N.103, G.114, K.117 No protein-ligand interaction detected (PLIP) NAG-NAG.40: 4 residues within 4Å: Chain B: R.278 Chain F: R.162, I.164, N.167 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:I.164 NAG-NAG.41: 4 residues within 4Å: Chain F: N.204, T.206, S.244, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG.42: 7 residues within 4Å: Chain F: H.55, K.199, N.211 Chain K: G.54, H.55, T.72, N.75 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:T.72 NAG-NAG.45: 3 residues within 4Å: Chain F: Q.263, N.265, T.301 No protein-ligand interaction detected (PLIP) NAG-NAG.46: 3 residues within 4Å: Chain F: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.47: 1 residues within 4Å: Chain F: N.324 No protein-ligand interaction detected (PLIP) NAG-NAG.48: 4 residues within 4Å: Chain F: N.355, S.357 Ligands: NAG-NAG-BMA.49, NAG.63 No protein-ligand interaction detected (PLIP) NAG-NAG.50: 4 residues within 4Å: Chain F: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.43 No protein-ligand interaction detected (PLIP)

9 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: 10 residues within 4Å: Chain A: G.16, S.17 Chain B: E.57, N.58 Chain G: R.104, P.105, W.106, N.107, I.108, L.112 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:N.107, G:N.107 NAG-NAG-BMA-MAN-MAN.10: 3 residues within 4Å: Chain B: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.17: 5 residues within 4Å: Chain B: V.104, N.106, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.20: 10 residues within 4Å: Chain C: G.16, S.17 Chain D: E.57, N.58 Chain I: R.104, P.105, W.106, N.107, I.108, L.112 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:N.107, I:N.107 NAG-NAG-BMA-MAN-MAN.27: 3 residues within 4Å: Chain D: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.34: 5 residues within 4Å: Chain D: V.104, N.106, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.37: 10 residues within 4Å: Chain E: G.16, S.17 Chain F: E.57, N.58 Chain K: R.104, P.105, W.106, N.107, I.108, L.112 2 PLIP interactions: 2 interactions with chain K Hydrogen bonds: K:N.107, K:N.107 NAG-NAG-BMA-MAN-MAN.44: 3 residues within 4Å: Chain F: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.51: 5 residues within 4Å: Chain F: V.104, N.106, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP)

6 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.5: 4 residues within 4Å: Chain B: Q.100, S.120, F.121, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 3 residues within 4Å: Chain B: S.357, N.361 Ligands: NAG-NAG.14 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 4 residues within 4Å: Chain D: Q.100, S.120, F.121, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.32: 3 residues within 4Å: Chain D: S.357, N.361 Ligands: NAG-NAG.31 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.39: 4 residues within 4Å: Chain F: Q.100, S.120, F.121, N.122 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.49: 3 residues within 4Å: Chain F: S.357, N.361 Ligands: NAG-NAG.48 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.9: 10 residues within 4Å: Chain B: K.35, E.181, V.224, L.231, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG.16 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.348 NAG-NAG-BMA-MAN-MAN-MAN.26: 10 residues within 4Å: Chain D: K.35, E.181, V.224, L.231, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG.33 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.348 NAG-NAG-BMA-MAN-MAN-MAN.43: 10 residues within 4Å: Chain F: K.35, E.181, V.224, L.231, N.232, N.346, G.348, V.414, S.415 Ligands: NAG-NAG.50 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:G.348

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

NAG.52: 3 residues within 4Å: Chain A: N.107, S.109, E.110 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.107, A:S.109, A:S.109 NAG.53: 1 residues within 4Å: Chain B: N.107 No protein-ligand interaction detected (PLIP) NAG.54: 1 residues within 4Å: Chain B: N.308 No protein-ligand interaction detected (PLIP) NAG.55: 7 residues within 4Å: Chain B: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG.14, NAG-NAG.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.332, B:S.333, B:S.357 NAG.56: 3 residues within 4Å: Chain C: N.107, S.109, E.110 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.107, C:S.109, C:S.109 NAG.57: 1 residues within 4Å: Chain D: N.107 No protein-ligand interaction detected (PLIP) NAG.58: 1 residues within 4Å: Chain D: N.308 No protein-ligand interaction detected (PLIP) NAG.59: 7 residues within 4Å: Chain D: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG.31, NAG-NAG.31 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.332, D:S.333, D:S.357 NAG.60: 3 residues within 4Å: Chain E: N.107, S.109, E.110 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.107, E:S.109, E:S.109 NAG.61: 1 residues within 4Å: Chain F: N.107 No protein-ligand interaction detected (PLIP) NAG.62: 1 residues within 4Å: Chain F: N.308 No protein-ligand interaction detected (PLIP) NAG.63: 7 residues within 4Å: Chain F: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG.48, NAG-NAG.48 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:N.332, F:S.333, F:S.357

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Reveiz, M. et al., Vaccine-elicited and naturally elicited antibodies differ in their recognition of the HIV-1 fusion peptide. Front Immunol (2024)

Release Date

2024-08-14

Peptides

Envelope glycoprotein gp41: ACE
Envelope glycoprotein gp120: BDF
antibody ACS202 Fab heavy chain: GIK
antibody ACS202 Fab light chain: HJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

C
A

E
F

B
G

D
C

F
I

G
H

I
D

K
J

H
L

J
E

L
K

Envelope glycoprotein gp41

Envelope glycoprotein gp120

antibody ACS202 Fab heavy chain

antibody ACS202 Fab light chain

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