SMTL ID : 6v0r.1

BG505 SOSIP.664 Trimer

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

12 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: E.57, N.58 Chain B: G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.246, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG.29 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain A: N.265, T.267, H.299, N.301, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain C: E.57, N.58 Chain D: G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 2 residues within 4Å: Chain C: N.246, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain C: N.355, S.357 Ligands: NAG.40 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 5 residues within 4Å: Chain C: N.265, T.267, H.299, N.301, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain E: E.57, N.58 Chain F: G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 2 residues within 4Å: Chain E: N.246, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain E: N.355, S.357 Ligands: NAG.51 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 5 residues within 4Å: Chain E: N.265, T.267, H.299, N.301, R.412 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.4: 11 residues within 4Å: Chain A: S.179, E.181, P.182, N.232, F.345, N.346, C.347, G.348, V.414, S.415 Ligands: NAG.32 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.348, A:V.414 NAG-NAG-BMA-MAN-MAN-MAN.13: 11 residues within 4Å: Chain C: S.179, E.181, P.182, N.232, F.345, N.346, C.347, G.348, V.414, S.415 Ligands: NAG.43 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.348, C:V.414 NAG-NAG-BMA-MAN-MAN-MAN.22: 11 residues within 4Å: Chain E: S.179, E.181, P.182, N.232, F.345, N.346, C.347, G.348, V.414, S.415 Ligands: NAG.54 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:G.348, E:V.414

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: 5 residues within 4Å: Chain A: V.104, N.118, Y.135, L.137, D.290 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.135 NAG-NAG-BMA.6: 2 residues within 4Å: Chain A: N.103, G.114 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 5 residues within 4Å: Chain C: V.104, N.118, Y.135, L.137, D.290 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.135 NAG-NAG-BMA.15: 2 residues within 4Å: Chain C: N.103, G.114 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.23: 5 residues within 4Å: Chain E: V.104, N.118, Y.135, L.137, D.290 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.135 NAG-NAG-BMA.24: 2 residues within 4Å: Chain E: N.103, G.114 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.7: 4 residues within 4Å: Chain A: N.106, N.107, G.293, D.294 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.16: 4 residues within 4Å: Chain C: N.106, N.107, G.293, D.294 No protein-ligand interaction detected (PLIP) NAG-NAG-FUC.25: 4 residues within 4Å: Chain E: N.106, N.107, G.293, D.294 No protein-ligand interaction detected (PLIP)

3 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-FUC.9: 6 residues within 4Å: Chain B: P.98, W.99, N.100, S.102, W.103, Y.127 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:P.98, B:Y.127 NAG-FUC.18: 6 residues within 4Å: Chain D: P.98, W.99, N.100, S.102, W.103, Y.127 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:P.98, D:Y.127 NAG-FUC.27: 6 residues within 4Å: Chain F: P.98, W.99, N.100, S.102, W.103, Y.127 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:P.98, F:Y.127

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

NAG.28: 2 residues within 4Å: Chain A: N.204, T.206 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain A: N.361 Ligands: NAG-NAG.3 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain A: N.308, T.363 Ligand excluded by PLIP NAG.31: 6 residues within 4Å: Chain A: Q.263, N.265, N.301, V.302, S.303, R.412 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain A: V.414, S.415, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.4 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: N.271, I.292, V.410 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain A: S.120, F.121, N.122 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain A: R.162, N.167, T.168 Chain C: R.278 Ligand excluded by PLIP NAG.36: 1 residues within 4Å: Chain A: N.324 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain B: N.107, S.109, E.110 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain B: K.122, E.123, N.126, Y.127 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.204, T.206 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain C: N.361 Ligands: NAG-NAG.12 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain C: N.308, T.363 Ligand excluded by PLIP NAG.42: 6 residues within 4Å: Chain C: Q.263, N.265, N.301, V.302, S.303, R.412 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain C: V.414, S.415, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.13 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain C: N.271, I.292, V.410 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: S.120, F.121, N.122 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain C: R.162, N.167, T.168 Chain E: R.278 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain C: N.324 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain D: N.107, S.109, E.110 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain D: K.122, E.123, N.126, Y.127 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain E: N.204, T.206 Ligand excluded by PLIP NAG.51: 2 residues within 4Å: Chain E: N.361 Ligands: NAG-NAG.21 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain E: N.308, T.363 Ligand excluded by PLIP NAG.53: 6 residues within 4Å: Chain E: Q.263, N.265, N.301, V.302, S.303, R.412 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain E: V.414, S.415, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.22 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain E: N.271, I.292, V.410 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain E: S.120, F.121, N.122 Ligand excluded by PLIP NAG.57: 4 residues within 4Å: Chain A: R.278 Chain E: R.162, N.167, T.168 Ligand excluded by PLIP NAG.58: 1 residues within 4Å: Chain E: N.324 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain F: N.107, S.109, E.110 Ligand excluded by PLIP NAG.60: 4 residues within 4Å: Chain F: K.122, E.123, N.126, Y.127 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nogal, B. et al., Mapping Polyclonal Antibody Responses in Non-human Primates Vaccinated with HIV Env Trimer Subunit Vaccines. Cell Rep (2020)

Release Date

2020-04-01

Peptides

BG505 SOSIPv5.2 gp120: ACE
BG505 SOSIPv5.2 gp41: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
D

B
B

D
E

F
F

BG505 SOSIPv5.2 gp120

BG505 SOSIPv5.2 gp41

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