SMTL ID : 6mdt.1

Crystal structure of the B41 SOSIP.664 Env trimer with PGT124 and 35O22 Fabs, in P63 space group

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.82 Å

Oligo State

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

Ligands

4 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.1: 12 residues within 4Å: Chain A: E.110, N.114, M.115 Chain C: E.1, G.2, Q.3, G.26, K.106, L.109, Y.119, L.120 Chain D: P.58 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain D Hydrogen bonds: C:Y.119, D:P.58, C:E.1, C:E.1, C:G.2, C:K.106, C:Y.119 Hydrophobic interactions: C:E.1 NAG-NAG-BMA-MAN-MAN.4: 3 residues within 4Å: Chain B: N.214, S.216, E.255 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.6: 7 residues within 4Å: Chain B: T.32, V.34, E.191, N.242, N.355, S.421, S.422 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.421 NAG-NAG-BMA-MAN-MAN.11: 5 residues within 4Å: Chain B: P.367, N.370, P.382, G.385, E.386 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.386 Hydrogen bonds: B:E.386, B:E.386

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-[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.2: 18 residues within 4Å: Chain A: S.17 Chain B: N.57 Chain C: N.30, F.31, Y.32, H.33, W.50, S.52, Y.54, S.55, D.57, K.58, N.59, R.110, D.111, G.112, T.115 Chain D: N.96 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:H.95, C:H.33

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.3: 4 residues within 4Å: Chain B: N.104, N.129, S.131, Y.146 No protein-ligand interaction detected (PLIP)

4 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: 4 residues within 4Å: Chain B: E.52, N.209, K.211, N.221 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.7: 9 residues within 4Å: Chain B: E.273, N.275, N.311, I.312, S.313, N.388 Ligands: NAG-NAG-BMA-MAN.12, NAG-NAG-BMA-MAN.12, NAG-NAG-BMA-MAN.12 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.9: 3 residues within 4Å: Chain B: N.340, H.341, S.343 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.13: 3 residues within 4Å: Chain B: A.271, E.273, N.423 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN: 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.8: 4 residues within 4Å: Chain B: N.281, T.283, I.302, R.415 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.415 NAG-NAG-BMA-MAN.10: 2 residues within 4Å: Chain B: N.364, T.366 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN: 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.12: 7 residues within 4Å: Chain B: N.275, N.388, R.419 Ligands: NAG-NAG-BMA.7, NAG-NAG-BMA.7, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.14, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.14 No protein-ligand interaction detected (PLIP)

1 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-(1-3)-[alpha-D-mannopyranose-(1-6)]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.14: 17 residues within 4Å: Chain B: T.277, H.309, N.311, R.419 Chain E: R.103, I.104, G.106, V.107, V.108 Chain F: S.25, N.45, Q.47, P.61, D.62, I.63 Ligands: NAG-NAG-BMA-MAN.12, NAG-NAG-BMA-MAN.12 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:V.108

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

NAG.15: 1 residues within 4Å: Chain A: N.105 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.105 NAG.16: 2 residues within 4Å: Chain A: N.100, S.102 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.102 NAG.17: 1 residues within 4Å: Chain A: N.126 No protein-ligand interaction detected (PLIP) NAG.18: 2 residues within 4Å: Chain B: N.99, N.133 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.131 NAG.19: 2 residues within 4Å: Chain B: R.172, N.177 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.172, B:R.172, B:N.177 NAG.20: 3 residues within 4Å: Chain B: N.256, T.258, D.259 No protein-ligand interaction detected (PLIP) NAG.21: 4 residues within 4Å: Chain B: K.314, N.318, W.373, P.382 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.318 NAG.22: 2 residues within 4Å: Chain B: N.374, N.375 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.374, B:N.375 NAG.23: 2 residues within 4Å: Chain B: N.334, K.335 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.335

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumar, S. et al., Capturing the inherent structural dynamics of the HIV-1 envelope glycoprotein fusion peptide. Nat Commun (2019)

Release Date

2019-02-27

Peptides

Transmembrane protein gp41: A
Surface protein gp120: B
35O22 Fab heavy chain: C
35O22 Fab light chain: D
PGT124 Fab heavy chain: E
PGT124 Fab light chain: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
G

C
D

D
E

E
H

F
L

Transmembrane protein gp41

Surface protein gp120

35O22 Fab heavy chain

35O22 Fab light chain

PGT124 Fab heavy chain

PGT124 Fab light chain

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