SMTL ID : 6ccb.1 (1 other biounit)

Crystal structure of 253-11 SOSIP trimer in complex with 10-1074 Fab

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 6.50 Å

Oligo State

hetero-3-3-3-3-mer

Ligands

3 x NAG- NAG- BMA- MAN- MAN- MAN: 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.1: 9 residues within 4Å: Chain B: E.37, E.183, P.184, N.234, N.348, G.350, E.419, S.420 Ligands: NAG.14 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.183, B:G.350 NAG-NAG-BMA-MAN-MAN-MAN.19: 9 residues within 4Å: Chain F: E.37, E.183, P.184, N.234, N.348, G.350, E.419, S.420 Ligands: NAG.32 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:E.183, F:G.350 NAG-NAG-BMA-MAN-MAN-MAN.37: 9 residues within 4Å: Chain J: E.37, E.183, P.184, N.234, N.348, G.350, E.419, S.420 Ligands: NAG.50 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:E.183, J:G.350

3 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.2: 18 residues within 4Å: Chain B: N.267, N.303, R.417 Chain C: Q.103, R.104, I.105, G.107, V.108, Y.117 Chain D: S.26, N.46, N.47, Q.48, D.49, D.63, I.64, N.65 Ligands: NAG.18 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.104, C:G.107 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.20: 18 residues within 4Å: Chain F: N.267, N.303, R.417 Chain G: Q.103, R.104, I.105, G.107, V.108, Y.117 Chain H: S.26, N.46, N.47, Q.48, D.49, D.63, I.64, N.65 Ligands: NAG.36 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:R.104, G:G.107 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.38: 18 residues within 4Å: Chain J: N.267, N.303, R.417 Chain K: Q.103, R.104, I.105, G.107, V.108, Y.117 Chain L: S.26, N.46, N.47, Q.48, D.49, D.63, I.64, N.65 Ligands: NAG.54 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:R.104, K:G.107

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

NAG.3: 1 residues within 4Å: Chain A: N.126 Ligand excluded by PLIP NAG.4: 2 residues within 4Å: Chain A: D.110, N.114 Ligand excluded by PLIP NAG.5: 4 residues within 4Å: Chain A: G.16, S.17 Chain B: E.60, N.61 Ligand excluded by PLIP NAG.6: 4 residues within 4Å: Chain B: F.107, N.127, D.144, A.292 Ligand excluded by PLIP NAG.7: 5 residues within 4Å: Chain B: S.129, F.130, N.131, K.142 Ligands: NAG.15 Ligand excluded by PLIP NAG.8: 3 residues within 4Å: Chain B: N.169, T.170 Chain J: R.280 Ligand excluded by PLIP NAG.9: 3 residues within 4Å: Chain B: N.206, T.208, S.246 Ligand excluded by PLIP NAG.10: 3 residues within 4Å: Chain B: D.202, K.212, N.213 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain B: N.248, T.250, D.251 Ligand excluded by PLIP NAG.12: 5 residues within 4Å: Chain B: N.334, A.335, N.357, S.359 Ligands: NAG.13 Ligand excluded by PLIP NAG.13: 5 residues within 4Å: Chain B: N.357, S.359, K.360, Q.390 Ligands: NAG.12 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain B: N.234, P.263, N.421 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.1 Ligand excluded by PLIP NAG.15: 4 residues within 4Å: Chain B: N.103, N.160, Y.162 Ligands: NAG.7 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain B: N.310, D.311, W.366 Ligand excluded by PLIP NAG.17: 4 residues within 4Å: Chain B: N.273, I.294, E.415 Chain D: F.66 Ligand excluded by PLIP NAG.18: 5 residues within 4Å: Chain B: N.265, N.267, N.303, S.305 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.2 Ligand excluded by PLIP NAG.21: 1 residues within 4Å: Chain E: N.126 Ligand excluded by PLIP NAG.22: 2 residues within 4Å: Chain E: D.110, N.114 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain E: G.16, S.17 Chain F: E.60, N.61 Ligand excluded by PLIP NAG.24: 4 residues within 4Å: Chain F: F.107, N.127, D.144, A.292 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain F: S.129, F.130, N.131, K.142 Ligands: NAG.33 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain B: R.280 Chain F: N.169, T.170 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain F: N.206, T.208, S.246 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain F: D.202, K.212, N.213 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain F: N.248, T.250, D.251 Ligand excluded by PLIP NAG.30: 5 residues within 4Å: Chain F: N.334, A.335, N.357, S.359 Ligands: NAG.31 Ligand excluded by PLIP NAG.31: 5 residues within 4Å: Chain F: N.357, S.359, K.360, Q.390 Ligands: NAG.30 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain F: N.234, P.263, N.421 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.19 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain F: N.103, N.160, Y.162 Ligands: NAG.25 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain F: N.310, D.311, W.366 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain F: N.273, I.294, E.415 Chain H: F.66 Ligand excluded by PLIP NAG.36: 5 residues within 4Å: Chain F: N.265, N.267, N.303, S.305 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.20 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain I: N.126 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain I: D.110, N.114 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain I: G.16, S.17 Chain J: E.60, N.61 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain J: F.107, N.127, D.144, A.292 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain J: S.129, F.130, N.131, K.142 Ligands: NAG.51 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain F: R.280 Chain J: N.169, T.170 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain J: N.206, T.208, S.246 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain J: D.202, K.212, N.213 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain J: N.248, T.250, D.251 Ligand excluded by PLIP NAG.48: 5 residues within 4Å: Chain J: N.334, A.335, N.357, S.359 Ligands: NAG.49 Ligand excluded by PLIP NAG.49: 5 residues within 4Å: Chain J: N.357, S.359, K.360, Q.390 Ligands: NAG.48 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain J: N.234, P.263, N.421 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.37 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain J: N.103, N.160, Y.162 Ligands: NAG.43 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain J: N.310, D.311, W.366 Ligand excluded by PLIP NAG.53: 4 residues within 4Å: Chain J: N.273, I.294, E.415 Chain L: F.66 Ligand excluded by PLIP NAG.54: 5 residues within 4Å: Chain J: N.265, N.267, N.303, S.305 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.38 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Moyo, T. et al., Molecular Basis of Unusually High Neutralization Resistance in Tier 3 HIV-1 Strain 253-11. J. Virol. (2018)

Release Date

2018-04-04

Peptides

Glycoprotein 41: AEI
Glycoprotein 120: BFJ
10-1074 FAB heavy chain: CGK
10-1074 Fab light chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

I
A

B
C

F
C

J
C

C
D

G
D

K
D

D
E

H
E

L
E

Glycoprotein 41

Glycoprotein 120

10-1074 FAB heavy chain

10-1074 Fab light chain

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