SMTL ID : 7t2p.2 (1 other biounit)

The Envelope Glycoprotein SIVmac239.K180S SOSIP trimer in complex with 3 copies of the neutralizing antibody K11

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[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.1: 18 residues within 4Å: Chain A: N.37, S.74, F.75, N.79, F.251, M.252, P.253, G.292, R.293, K.498 Chain C: N.125, F.126, Y.128 Chain D: N.71, G.85, S.86 Ligands: NAG-NAG.8, NAG.14 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.251 Hydrogen bonds: A:S.74

5 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: 3 residues within 4Å: Chain A: N.114, E.117, R.120 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 11 residues within 4Å: Chain A: G.292, R.293, D.294, N.295, R.366, T.368, W.472, I.473, D.474 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.368 NAG-NAG.9: 2 residues within 4Å: Chain A: N.316, D.456 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 8 residues within 4Å: Chain A: I.152, A.153, R.312, W.345, R.396, T.458, N.460 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.152, A:A.153 Hydrogen bonds: A:R.312 NAG-NAG.12: 3 residues within 4Å: Chain A: D.471, Q.477, N.479 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.3: 3 residues within 4Å: Chain A: M.144, N.146, T.148 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:M.144 NAG-NAG-FUC.4: 2 residues within 4Å: Chain A: Q.154, N.156 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.5: 6 residues within 4Å: Chain A: V.193, C.194, E.195, Q.196, N.212, T.213 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.196

1 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.6: 11 residues within 4Å: Chain A: K.222, W.225, D.226, Q.270, N.278, N.394, R.396, C.459, N.460, S.461 Ligands: NAG-NAG.11 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.460 Hydrogen bonds: A:W.225, A:N.460

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.7: 6 residues within 4Å: Chain A: N.284, N.302, Y.304, Y.305, E.356 Chain C: M.94 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.304, A:Y.305

1 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.10: 9 residues within 4Å: Chain A: K.358, T.373, D.374, I.376, N.377, E.412, D.413, R.414, N.415 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.412, A:D.413

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

NAG.13: 3 residues within 4Å: Chain A: N.70 Chain B: G.15, S.16 No protein-ligand interaction detected (PLIP) NAG.14: 4 residues within 4Å: Chain A: N.79, R.293 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.79 NAG.15: 2 residues within 4Å: Chain A: R.112, N.171 No protein-ligand interaction detected (PLIP) NAG.16: 3 residues within 4Å: Chain A: E.182, Y.183, N.184 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.182 Hydrogen bonds: A:N.184 NAG.17: 2 residues within 4Å: Chain A: G.197, N.198 No protein-ligand interaction detected (PLIP) NAG.18: 2 residues within 4Å: Chain A: G.201, N.202 No protein-ligand interaction detected (PLIP) NAG.19: 4 residues within 4Å: Chain A: E.66, A.68, N.244, V.259 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.259 NAG.20: 3 residues within 4Å: Chain A: Y.304, N.306, K.349 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.306 NAG.21: 3 residues within 4Å: Chain A: D.474, N.476, Q.477 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.477 Hydrogen bonds: A:D.474, A:D.474 NAG.22: 1 residues within 4Å: Chain A: N.371 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.371 NAG.23: 6 residues within 4Å: Chain B: P.99, N.100, S.102, F.121, L.122 Ligands: NAG.25 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.102 NAG.24: 4 residues within 4Å: Chain B: K.106, W.107, N.108, N.109 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:K.106, B:N.108 Hydrogen bonds: B:N.109 NAG.25: 4 residues within 4Å: Chain B: F.121, L.122, N.125 Ligands: NAG.23 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, F. et al., Molecular insights into antibody-mediated protection against the prototypic simian immunodeficiency virus. Nat Commun (2022)

Release Date

2022-10-19

Peptides

Envelope glycoprotein gp120: A
Envelope glycoprotein gp41: B
K11 Fab heavy chain: C
K11 Fab light chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
H

D
L

Envelope glycoprotein gp120

Envelope glycoprotein gp41

K11 Fab heavy chain

K11 Fab light chain

Related Entries With Identical Sequence