SMTL ID : 5um8.1

Crystal structure of HIV-1 envelope trimer 16055 NFL TD CC (T569G) in complex with Fabs 35022 and PGT124

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.94 Å

Oligo State

hetero-1-1-1-1-1-1-mer

Ligands

8 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: 2 residues within 4Å: Chain A: N.361 Ligands: NAG-NAG.3 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.12 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG-NAG.1 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain A: N.205, P.209, S.245 Chain E: V.78 Ligands: NAG-NAG.7 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain A: V.149, R.163, I.165, N.168, T.169 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.165 NAG-NAG.7: 7 residues within 4Å: Chain A: N.201, T.203, F.204, P.209, C.210, N.211 Ligands: NAG-NAG.4 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain A: N.329, T.363, T.433 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain A: N.272, T.274, I.293 No protein-ligand interaction detected (PLIP)

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.6: 5 residues within 4Å: Chain A: N.105, N.123, S.125, Y.140 Chain C: R.92 No protein-ligand interaction detected (PLIP)

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.8: 3 residues within 4Å: Chain A: E.53, N.200, N.212 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- 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-(1-6)-[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-MAN-MAN-MAN.10: 15 residues within 4Å: Chain A: T.268, Y.300, N.302, T.383 Chain C: S.25, N.45, N.46, Q.47, P.61, D.62, I.63 Chain D: Q.102, R.103, G.106, V.108 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:V.108

1 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

NAG-NAG-BMA-MAN-MAN-MAN-MAN.11: 20 residues within 4Å: Chain A: E.57, N.58 Chain B: G.16, S.17 Chain E: N.30, F.31, Y.32, H.33, S.52, Y.54, S.55, D.57, N.59, R.110, D.111, G.112, S.113, T.115 Chain F: H.95, N.96 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:H.33, E:S.52, E:G.112, E:G.112

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-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.12: 9 residues within 4Å: Chain A: E.34, P.183, L.232, N.233, N.346, R.348, K.414, S.415 Ligands: NAG-NAG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.348, A:E.34

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

NAG.14: 5 residues within 4Å: Chain A: G.239, I.241, N.260, R.314, K.318 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.260, A:R.314 NAG.15: 3 residues within 4Å: Chain A: R.297, N.410, T.412 No protein-ligand interaction detected (PLIP) NAG.16: 2 residues within 4Å: Chain A: P.366, N.367 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.367 NAG.17: 3 residues within 4Å: Chain A: T.98, E.100, N.127 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.100 Hydrogen bonds: A:N.127 NAG.18: 3 residues within 4Å: Chain A: N.247, T.249, N.250 No protein-ligand interaction detected (PLIP) NAG.19: 3 residues within 4Å: Chain A: P.324, S.430, N.431 No protein-ligand interaction detected (PLIP) NAG.20: 2 residues within 4Å: Chain B: R.122, N.126 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.126 NAG.21: 3 residues within 4Å: Chain B: N.100, S.102, L.134 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.100, B:S.102 NAG.22: 10 residues within 4Å: Chain B: K.106, E.110, N.114, M.115 Chain E: E.1, Y.32, K.106, G.107, L.108, Y.119 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:E.1, E:E.1, E:Y.32, E:K.106, E:G.107

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guenaga, J. et al., Glycine Substitution at Helix-to-Coil Transitions Facilitates the Structural Determination of a Stabilized Subtype C HIV Envelope Glycoprotein. Immunity (2017)

Release Date

2017-05-24

Peptides

glycoprotein gp120: A
glycoprotein gp41: B
Fab PGT124 light chain: C
Fab PGT124 heavy chain: D
Fab 35022 heavy chain: E
Fab 35022 light chain: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

B
B

C
L

D
H

E
D

F
E

glycoprotein gp120

glycoprotein gp41

Fab PGT124 light chain

Fab PGT124 heavy chain

Fab 35022 heavy chain

Fab 35022 light chain

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