SMTL ID : 7kmd.1

Crystal structure of a HIV-1 clade C isolate Du172.17 HR1.R4.664 Env trimer in complex with human Fabs PGT124 and 35O22

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.39 Å

Oligo State

hetero-1-1-1-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-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-MAN-MAN-MAN-MAN-MAN.1: 21 residues within 4Å: Chain A: N.30, F.31, H.33, W.50, S.52, Y.54, D.57, K.58, N.59, L.60, R.110, D.111, G.112, S.113, T.115 Chain B: H.95, N.96 Chain C: K.56, N.57 Chain D: L.9, S.17 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.112, A:T.115, B:H.95, A:H.33, A:S.52

3 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.2: 5 residues within 4Å: Chain C: K.104, N.128, Y.145, D.298, I.299 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain C: N.212, T.214, G.215, P.216 Ligands: NAG-NAG-BMA.3 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 6 residues within 4Å: Chain C: V.54, N.207, K.209, N.219, V.220, S.221 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.209

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.3: 7 residues within 4Å: Chain A: V.76 Chain C: N.208, T.210, F.211, N.212, N.218 Ligands: NAG-NAG.4 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.8: 5 residues within 4Å: Chain C: E.247, N.267, E.268, R.321, E.324 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 3 residues within 4Å: Chain C: V.153, R.170, N.175 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 9 residues within 4Å: Chain A: E.1, Y.32, L.108, L.109 Chain B: P.58 Chain D: E.97, N.101, M.102, Q.106 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.1, A:E.1

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN-MAN-MAN.5: 19 residues within 4Å: Chain C: T.275, H.307, N.309, N.380, T.382 Chain E: N.45, N.46, Q.47, P.61, D.62, I.63, N.64 Chain F: R.103, I.104, Y.105, G.106, V.107, V.108 Ligands: NAG.13 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:V.107, F:V.108 Hydrogen bonds: F:V.108

1 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.6: 6 residues within 4Å: Chain C: E.271, N.273, N.309, I.310, S.311, K.413 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- NAG- BMA- MAN- NAG: 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-(6-8)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG-BMA-MAN-NAG.7: 10 residues within 4Å: Chain C: D.189, P.190, V.232, N.240, S.269, N.353, R.355, K.413, S.414, N.415 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.355

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

NAG.12: 2 residues within 4Å: Chain C: N.99, S.166 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:S.166 NAG.13: 3 residues within 4Å: Chain C: A.379, N.380 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.5 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.379 NAG.14: 3 residues within 4Å: Chain C: P.277, N.409 Ligands: NAG.15 No protein-ligand interaction detected (PLIP) NAG.15: 3 residues within 4Å: Chain C: N.279, I.300 Ligands: NAG.14 No protein-ligand interaction detected (PLIP) NAG.16: 1 residues within 4Å: Chain C: N.132 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.132 NAG.17: 2 residues within 4Å: Chain C: N.254, N.257 No protein-ligand interaction detected (PLIP) NAG.18: 2 residues within 4Å: Chain C: N.368, M.372 No protein-ligand interaction detected (PLIP) NAG.19: 2 residues within 4Å: Chain D: N.87, S.89 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.89 NAG.20: 1 residues within 4Å: Chain D: N.113 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, S. et al., Neutralizing Antibodies Induced by First-Generation gp41-Stabilized HIV-1 Envelope Trimers and Nanoparticles. Mbio (2021)

Release Date

2021-07-07

Peptides

35O22 Heavy chain: A
35O22 Light chain: B
Envelope glycoprotein gp120: C
Envelope glycoprotein gp41: D
124 Light chain: E
124 Heavy chain: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

C
G

D
T

E
L

F
H

35O22 Heavy chain

35O22 Light chain

Envelope glycoprotein gp120

Envelope glycoprotein gp41

124 Light chain

124 Heavy chain

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