SMTL ID : 6ohy.1

Chimpanzee SIV Env trimeric ectodomain.

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

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

NAG-FUC.1: 2 residues within 4Å: Chain A: P.56, N.57 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:P.56 Hydrogen bonds: A:N.57 NAG-FUC.9: 1 residues within 4Å: Chain A: N.359 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.359 NAG-FUC.13: 4 residues within 4Å: Chain B: R.120, E.121, N.123, N.124 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.121, B:N.123, B:N.124 NAG-FUC.14: 1 residues within 4Å: Chain B: N.102 No protein-ligand interaction detected (PLIP) NAG-FUC.15: 2 residues within 4Å: Chain C: P.56, N.57 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:P.56 Hydrogen bonds: C:N.57 NAG-FUC.23: 1 residues within 4Å: Chain C: N.359 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.359 NAG-FUC.27: 4 residues within 4Å: Chain D: R.120, E.121, N.123, N.124 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.120, D:N.123, D:N.124 NAG-FUC.28: 1 residues within 4Å: Chain D: N.102 No protein-ligand interaction detected (PLIP) NAG-FUC.29: 2 residues within 4Å: Chain E: P.56, N.57 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:P.56 Hydrogen bonds: E:N.57 NAG-FUC.37: 1 residues within 4Å: Chain E: N.359 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.359 NAG-FUC.41: 4 residues within 4Å: Chain F: R.120, E.121, N.123, N.124 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:E.121, F:N.123, F:N.124 NAG-FUC.42: 1 residues within 4Å: Chain F: N.102 No protein-ligand interaction detected (PLIP)

24 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: 1 residues within 4Å: Chain A: N.125 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: P.103, T.104, N.121, Y.138 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: N.344, S.346 Ligands: NAG-NAG.10 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain A: N.200, I.238, D.239, P.240, I.312 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.312 NAG-NAG.7: 3 residues within 4Å: Chain A: E.52, N.193, N.205 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 6 residues within 4Å: Chain A: E.347, N.350, T.352, K.353, K.356 Ligands: NAG-NAG.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:K.353 NAG-NAG.11: 6 residues within 4Å: Chain A: N.294, T.296, Q.297, E.358, N.359, M.360 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain A: N.226, P.252, N.395 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.8 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 1 residues within 4Å: Chain C: N.125 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain C: P.103, T.104, N.121, Y.138 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain C: N.344, S.346 Ligands: NAG-NAG.24 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 5 residues within 4Å: Chain C: N.200, I.238, D.239, P.240, I.312 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:I.312 NAG-NAG.21: 3 residues within 4Å: Chain C: E.52, N.193, N.205 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 6 residues within 4Å: Chain C: E.347, N.350, T.352, K.353, K.356 Ligands: NAG-NAG.19 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:K.353 NAG-NAG.25: 6 residues within 4Å: Chain C: N.294, T.296, Q.297, E.358, N.359, M.360 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 4 residues within 4Å: Chain C: N.226, P.252, N.395 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.22 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 1 residues within 4Å: Chain E: N.125 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 4 residues within 4Å: Chain E: P.103, T.104, N.121, Y.138 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 3 residues within 4Å: Chain E: N.344, S.346 Ligands: NAG-NAG.38 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 5 residues within 4Å: Chain E: N.200, I.238, D.239, P.240, I.312 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:I.312 NAG-NAG.35: 3 residues within 4Å: Chain E: E.52, N.193, N.205 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 6 residues within 4Å: Chain E: E.347, N.350, T.352, K.353, K.356 Ligands: NAG-NAG.33 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:K.353 NAG-NAG.39: 6 residues within 4Å: Chain E: N.294, T.296, Q.297, E.358, N.359, M.360 No protein-ligand interaction detected (PLIP) NAG-NAG.40: 4 residues within 4Å: Chain E: N.226, P.252, N.395 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.36 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.4: 5 residues within 4Å: Chain A: T.147, A.148, I.149, R.156, N.161 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.148 Hydrophobic interactions: A:T.147 NAG-NAG-FUC.18: 5 residues within 4Å: Chain C: T.147, A.148, I.149, R.156, N.161 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.148 Hydrophobic interactions: C:T.147 NAG-NAG-FUC.32: 5 residues within 4Å: Chain E: T.147, A.148, I.149, R.156, N.161 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:A.148 Hydrophobic interactions: E:T.147

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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-MAN.8: 13 residues within 4Å: Chain A: Y.30, H.35, N.36, P.176, V.218, L.225, N.226, N.335, C.336, R.387, T.393, S.394 Ligands: NAG-NAG.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.336 NAG-NAG-BMA-MAN-MAN-MAN-MAN.22: 13 residues within 4Å: Chain C: Y.30, H.35, N.36, P.176, V.218, L.225, N.226, N.335, C.336, R.387, T.393, S.394 Ligands: NAG-NAG.26 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:C.336 NAG-NAG-BMA-MAN-MAN-MAN-MAN.36: 13 residues within 4Å: Chain E: Y.30, H.35, N.36, P.176, V.218, L.225, N.226, N.335, C.336, R.387, T.393, S.394 Ligands: NAG-NAG.40 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:C.336

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

NAG.43: 1 residues within 4Å: Chain A: N.152 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain A: I.195, N.232, Q.233 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain A: N.262, G.284 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain A: N.303 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain A: R.314, N.316, Q.416 Ligands: NAG.49 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain A: R.287, N.389, I.390 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain A: E.412, Q.416, N.417 Ligands: NAG.47 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain B: V.108, N.112 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain C: N.152 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain C: I.195, N.232, Q.233 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain C: N.262, G.284 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain C: N.303 Ligand excluded by PLIP NAG.55: 4 residues within 4Å: Chain C: R.314, N.316, Q.416 Ligands: NAG.57 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain C: R.287, N.389, I.390 Ligand excluded by PLIP NAG.57: 4 residues within 4Å: Chain C: E.412, Q.416, N.417 Ligands: NAG.55 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain D: V.108, N.112 Ligand excluded by PLIP NAG.59: 1 residues within 4Å: Chain E: N.152 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain E: I.195, N.232, Q.233 Ligand excluded by PLIP NAG.61: 2 residues within 4Å: Chain E: N.262, G.284 Ligand excluded by PLIP NAG.62: 1 residues within 4Å: Chain E: N.303 Ligand excluded by PLIP NAG.63: 4 residues within 4Å: Chain E: R.314, N.316, Q.416 Ligands: NAG.65 Ligand excluded by PLIP NAG.64: 3 residues within 4Å: Chain E: R.287, N.389, I.390 Ligand excluded by PLIP NAG.65: 4 residues within 4Å: Chain E: E.412, Q.416, N.417 Ligands: NAG.63 Ligand excluded by PLIP NAG.66: 2 residues within 4Å: Chain F: V.108, N.112 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Andrabi, R. et al., The Chimpanzee SIV Envelope Trimer: Structure and Deployment as an HIV Vaccine Template. Cell Rep (2019)

Release Date

2019-06-05

Peptides

Envelope glycoprotein gp160: ACE
Envelope glycoprotein gp160: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
D

B
B

D
E

F
F

Envelope glycoprotein gp160

Envelope glycoprotein gp160