SMTL ID : 4zmj.1

Crystal Structure of Ligand-Free BG505 SOSIP.664 HIV-1 Env Trimer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.31 Å

Oligo State

hetero-3-3-mer

Ligands

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.1: 13 residues within 4Å: Chain A: K.35, S.179, E.181, L.231, N.232, N.346, G.348, I.407, Q.408, C.413, V.414, S.415 Ligands: NAG.11 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.348 NAG-NAG-BMA-MAN-MAN-MAN.19: 13 residues within 4Å: Chain C: K.35, S.179, E.181, L.231, N.232, N.346, G.348, I.407, Q.408, C.413, V.414, S.415 Ligands: NAG.29 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.348 NAG-NAG-BMA-MAN-MAN-MAN.37: 13 residues within 4Å: Chain E: K.35, S.179, E.181, L.231, N.232, N.346, G.348, I.407, Q.408, C.413, V.414, S.415 Ligands: NAG.47 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.348

6 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: 4 residues within 4Å: Chain A: V.144, R.162, N.167 Chain E: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain A: T.267, H.299, N.301, D.380, S.381, T.383 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain A: R.278 Chain C: V.144, R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 6 residues within 4Å: Chain C: T.267, H.299, N.301, D.380, S.381, T.383 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 4 residues within 4Å: Chain C: R.278 Chain E: V.144, R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.39: 6 residues within 4Å: Chain E: T.267, H.299, N.301, D.380, S.381, T.383 No protein-ligand interaction detected (PLIP)

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

NAG.4: 3 residues within 4Å: Chain A: N.204, T.206, S.244 Ligand excluded by PLIP NAG.5: 3 residues within 4Å: Chain A: N.246, T.248, N.249 Ligand excluded by PLIP NAG.6: 2 residues within 4Å: Chain A: N.308, W.364 Ligand excluded by PLIP NAG.7: 1 residues within 4Å: Chain A: N.324 Ligand excluded by PLIP NAG.8: 6 residues within 4Å: Chain A: N.332, S.333, N.355, S.357 Ligands: NAG.9, NAG.10 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG.8 Ligand excluded by PLIP NAG.10: 2 residues within 4Å: Chain A: N.361 Ligands: NAG.8 Ligand excluded by PLIP NAG.11: 4 residues within 4Å: Chain A: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.1 Ligand excluded by PLIP NAG.12: 3 residues within 4Å: Chain A: N.118, S.120, Y.135 Ligand excluded by PLIP NAG.13: 6 residues within 4Å: Chain A: T.98, Q.100, S.120, N.122, K.131, K.133 Ligand excluded by PLIP NAG.14: 5 residues within 4Å: Chain A: Q.263, N.265, V.302, S.303, R.412 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.271, I.292, V.410 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain B: N.100, S.102 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain B: N.107 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain B: E.123, N.126 Ligand excluded by PLIP NAG.22: 3 residues within 4Å: Chain C: N.204, T.206, S.244 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain C: N.246, T.248, N.249 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain C: N.308, W.364 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain C: N.324 Ligand excluded by PLIP NAG.26: 6 residues within 4Å: Chain C: N.332, S.333, N.355, S.357 Ligands: NAG.27, NAG.28 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain C: N.355, S.357 Ligands: NAG.26 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain C: N.361 Ligands: NAG.26 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain C: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.19 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain C: N.118, S.120, Y.135 Ligand excluded by PLIP NAG.31: 6 residues within 4Å: Chain C: T.98, Q.100, S.120, N.122, K.131, K.133 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain C: Q.263, N.265, V.302, S.303, R.412 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain C: N.271, I.292, V.410 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain D: N.100, S.102 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain D: N.107 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain D: E.123, N.126 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain E: N.204, T.206, S.244 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain E: N.246, T.248, N.249 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain E: N.308, W.364 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain E: N.324 Ligand excluded by PLIP NAG.44: 6 residues within 4Å: Chain E: N.332, S.333, N.355, S.357 Ligands: NAG.45, NAG.46 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain E: N.355, S.357 Ligands: NAG.44 Ligand excluded by PLIP NAG.46: 2 residues within 4Å: Chain E: N.361 Ligands: NAG.44 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain E: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.37 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain E: N.118, S.120, Y.135 Ligand excluded by PLIP NAG.49: 6 residues within 4Å: Chain E: T.98, Q.100, S.120, N.122, K.131, K.133 Ligand excluded by PLIP NAG.50: 5 residues within 4Å: Chain E: Q.263, N.265, V.302, S.303, R.412 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain E: N.271, I.292, V.410 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain F: N.100, S.102 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain F: N.107 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain F: E.123, N.126 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Do Kwon, Y. et al., Crystal structure, conformational fixation and entry-related interactions of mature ligand-free HIV-1 Env. Nat.Struct.Mol.Biol. (2015)

Release Date

2015-06-24

Peptides

Envelope glycoprotein gp160: ACE
Envelope glycoprotein gp160: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

C
G

E
G

B
B

D
B

F
B

Envelope glycoprotein gp160

Envelope glycoprotein gp160

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