SMTL ID : 4nco.1

Crystal Structure of the BG505 SOSIP gp140 HIV-1 Env trimer in Complex with the Broadly Neutralizing Fab PGT122

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 4.70 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

12 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: 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(Post Translational Modification)(Non-covalent)

NAG-NAG-BMA-MAN-MAN-MAN-MAN.1: 9 residues within 4Å: Chain A: N.107, I.108, T.109 Chain D: Y.50, S.54, G.55, D.56, T.57, N.58 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:N.58 Hydrogen bonds: D:Y.50, D:D.56 NAG-NAG-BMA-MAN-MAN-MAN-MAN.2: 7 residues within 4Å: Chain A: T.102, N.118, S.120, K.133, Y.135, G.289, I.291 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.133 NAG-NAG-BMA-MAN-MAN-MAN-MAN.3: 9 residues within 4Å: Chain A: S.179, E.181, P.182, K.222, V.224, N.232, V.414, S.415 Ligands: NAG.28 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.179, A:S.179 NAG-NAG-BMA-MAN-MAN-MAN-MAN.4: 5 residues within 4Å: Chain A: N.271, N.272, T.273, I.292 Chain C: F.62 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.7: 9 residues within 4Å: Chain E: N.107, I.108, T.109 Chain H: Y.50, S.54, G.55, D.56, T.57, N.58 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:Y.50 NAG-NAG-BMA-MAN-MAN-MAN-MAN.8: 7 residues within 4Å: Chain E: T.102, N.118, S.120, K.133, Y.135, G.289, I.291 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.133 NAG-NAG-BMA-MAN-MAN-MAN-MAN.9: 9 residues within 4Å: Chain E: S.179, E.181, P.182, K.222, V.224, N.232, V.414, S.415 Ligands: NAG.38 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:S.179, E:S.179 NAG-NAG-BMA-MAN-MAN-MAN-MAN.10: 5 residues within 4Å: Chain E: N.271, T.273, I.292, V.410 Chain G: F.62 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.13: 6 residues within 4Å: Chain I: N.107, I.108, T.109 Chain L: S.54, T.57, N.58 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.14: 6 residues within 4Å: Chain I: T.102, N.118, K.133, Y.135, G.289, I.291 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:K.133 NAG-NAG-BMA-MAN-MAN-MAN-MAN.15: 9 residues within 4Å: Chain I: S.179, E.181, P.182, K.222, V.224, N.232, V.414, S.415 Ligands: NAG.48 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:S.179, I:S.179 NAG-NAG-BMA-MAN-MAN-MAN-MAN.16: 7 residues within 4Å: Chain I: N.271, N.272, T.273, I.291, I.292, V.410 Chain K: F.62 No protein-ligand interaction detected (PLIP)

3 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-(1-2)-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(Post Translational Modification)

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.5: 9 residues within 4Å: Chain A: N.265, N.301, S.381, T.383 Chain D: G.106, V.107, V.108 Ligands: MAN-MAN.6, NAG.24 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.106, D:V.107 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.11: 8 residues within 4Å: Chain E: N.265, N.301, S.381, T.383 Chain H: G.106, V.108 Ligands: MAN-MAN.12, NAG.34 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:G.106 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.17: 11 residues within 4Å: Chain I: N.265, N.301, S.381, T.383 Chain L: I.104, Y.105, G.106, V.107, V.108 Ligands: MAN-MAN.18, NAG.44 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:G.106, L:V.107

3 x MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose(Non-covalent)

MAN-MAN.6: 6 residues within 4Å: Chain C: N.42 Chain D: R.102, R.103, I.104, Y.116 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.5 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.103, D:Y.116, D:Y.116, C:N.42 MAN-MAN.12: 6 residues within 4Å: Chain G: N.42 Chain H: R.102, R.103, I.104, Y.116 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.11 5 PLIP interactions: 2 interactions with chain G, 3 interactions with chain H Hydrogen bonds: G:N.42, G:D.45, H:R.103, H:Y.116, H:Y.116 MAN-MAN.18: 6 residues within 4Å: Chain K: N.42 Chain L: R.102, R.103, I.104, Y.116 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.17 4 PLIP interactions: 3 interactions with chain L, 1 interactions with chain K Hydrogen bonds: L:R.103, L:Y.116, L:Y.116, K:N.42

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

NAG.19: 2 residues within 4Å: Chain A: E.57, N.58 Ligand excluded by PLIP NAG.20: 3 residues within 4Å: Chain A: Q.100, N.122, K.131 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain A: N.167 Chain I: I.279 Ligand excluded by PLIP NAG.22: 1 residues within 4Å: Chain A: N.204 Ligand excluded by PLIP NAG.23: 3 residues within 4Å: Chain A: N.246, T.248, N.249 Ligand excluded by PLIP NAG.24: 7 residues within 4Å: Chain A: Q.263, N.265, N.301, V.302, S.303, S.381 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.5 Ligand excluded by PLIP NAG.25: 2 residues within 4Å: Chain A: R.319, N.324 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: N.332, N.355, S.357 Ligands: NAG.27 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: S.357, N.361 Ligands: NAG.26 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain A: P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.3 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain E: E.57, N.58 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain E: Q.100, N.122, K.131 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain A: I.279 Chain E: N.167 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain E: N.204, T.206 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain E: N.246, T.248, N.249 Ligand excluded by PLIP NAG.34: 7 residues within 4Å: Chain E: Q.263, N.265, N.301, V.302, S.303, S.381 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.11 Ligand excluded by PLIP NAG.35: 2 residues within 4Å: Chain E: R.319, N.324 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain E: N.332, N.355, S.357 Ligands: NAG.37 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain E: S.357, N.361 Ligands: NAG.36 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain E: P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.9 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain I: E.57, N.58 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain I: Q.100, N.122, K.131 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain I: N.167 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain I: N.204 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain I: N.246, T.248, N.249 Ligand excluded by PLIP NAG.44: 7 residues within 4Å: Chain I: Q.263, N.265, N.301, V.302, S.303, S.381 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.17 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain I: R.319, N.324 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain I: N.332, N.355, S.357 Ligands: NAG.47 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain I: S.357, N.361 Ligands: NAG.46 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain I: P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.15 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Julien, J.P. et al., Crystal structure of a soluble cleaved HIV-1 envelope trimer. Science (2013)

Release Date

2013-11-13

Peptides

BG505 SOSIP gp120: AEI
BG505 SOSIP gp41: BFJ
PGT122 light chain: CGK
PGT122 heavy chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

I
I

B
B

F
F

J
J

C
C

G
G

K
K

D
D

H
H

L
L

BG505 SOSIP gp120

BG505 SOSIP gp41

PGT122 light chain

PGT122 heavy chain

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