SMTL ID : 5wdu.1

HIV-1 Env BG505 SOSIP.664 H72C-H564C trimer in complex with bNAbs PGT122 Fab, 35O22 Fab and NIH45-46 scFv

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 7.00 Å

Oligo State

hetero-3-3-3-3-3-3-3-mer

Ligands

9 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: 13 residues within 4Å: Chain A: N.57 Chain G: S.11 Chain J: N.30, F.31, S.52, Y.54, S.55, R.110, D.111, G.112, S.113, T.115 Chain K: H.94 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:T.115, J:S.55, J:D.111 Hydrophobic interactions: J:Y.54 NAG-NAG-BMA-MAN-MAN.3: 5 residues within 4Å: Chain A: V.103, T.104, N.117, S.119, Y.134 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.8: 3 residues within 4Å: Chain A: N.270, T.272, I.291 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.10: 12 residues within 4Å: Chain C: E.56, N.57 Chain L: L.3 Chain O: N.30, F.31, Y.32, H.33, S.52, D.57, R.110 Chain P: H.94, N.95 2 PLIP interactions: 2 interactions with chain O Hydrogen bonds: O:S.52, O:S.52 NAG-NAG-BMA-MAN-MAN.12: 4 residues within 4Å: Chain C: T.104, N.117, S.119, Y.134 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.17: 2 residues within 4Å: Chain C: N.270, I.291 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.19: 11 residues within 4Å: Chain E: E.56, N.57 Chain Q: L.3, S.11 Chain T: N.30, S.52, Y.54, S.55, D.111, G.112 Chain U: H.94 1 PLIP interactions: 1 interactions with chain T Hydrogen bonds: T:D.111 NAG-NAG-BMA-MAN-MAN.21: 4 residues within 4Å: Chain E: T.104, N.117, S.119, Y.134 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.26: 2 residues within 4Å: Chain E: N.270, I.291 No protein-ligand interaction detected (PLIP)

3 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.2: 6 residues within 4Å: Chain A: N.106, I.107 Chain H: D.89, T.94 Chain I: N.58, F.114 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.11: 6 residues within 4Å: Chain C: N.106, I.107 Chain M: T.94 Chain N: Y.50, N.58, F.114 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.20: 5 residues within 4Å: Chain E: N.106, I.107 Chain R: T.94 Chain S: N.58, F.114 No protein-ligand interaction detected (PLIP)

3 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.4: 6 residues within 4Å: Chain A: R.161, C.165, N.166, T.167 Chain B: D.73, Y.75 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.75 NAG-NAG-BMA-MAN.13: 5 residues within 4Å: Chain C: C.165, N.166, T.167 Chain D: D.73, Y.75 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:D.73, D:Y.75 Hydrogen bonds: D:D.73 NAG-NAG-BMA-MAN.22: 6 residues within 4Å: Chain E: R.161, C.165, N.166, T.167 Chain F: D.73, Y.75 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:D.73

3 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.5: 4 residues within 4Å: Chain A: N.203, T.205, S.243 Chain J: V.78 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.168, B:S.168 NAG-NAG-BMA-MAN-MAN-MAN-MAN.14: 7 residues within 4Å: Chain C: N.203, T.205, S.243, I.246 Chain D: R.204, G.206 Chain O: V.78 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN-MAN.23: 7 residues within 4Å: Chain E: N.203, T.205, S.243, I.246 Chain F: S.168, R.204 Chain T: P.77 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:S.168, F:S.168

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.6: 9 residues within 4Å: Chain A: K.34, P.181, V.223, N.231, N.345, C.346, G.347, Q.407, S.414 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.347 NAG-NAG-BMA-MAN-MAN-MAN.15: 6 residues within 4Å: Chain C: K.34, E.180, P.181, V.223, N.231, S.414 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.24: 6 residues within 4Å: Chain E: E.180, P.181, N.231, R.411, C.412, S.414 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.7: 6 residues within 4Å: Chain A: Q.262, N.264, N.300, V.301, S.302, S.380 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 6 residues within 4Å: Chain C: Q.262, N.264, N.300, V.301, S.302, S.380 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 6 residues within 4Å: Chain E: Q.262, N.264, N.300, V.301, S.302, S.380 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN: 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.9: 13 residues within 4Å: Chain A: T.266, H.298, N.300, D.379, T.382 Chain H: N.45, P.60, G.61 Chain I: R.103, I.104, G.106, V.107, V.108 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain I Hydrogen bonds: A:R.295, I:V.107, I:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.18: 15 residues within 4Å: Chain C: T.266, R.295, H.298, N.300, D.379, T.382 Chain M: N.45, P.60, G.61, S.62 Chain N: R.103, I.104, G.106, V.107, V.108 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.295 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN.27: 13 residues within 4Å: Chain E: T.266, H.298, N.300, D.379, T.382 Chain R: N.45, P.60, G.61, S.62 Chain S: R.103, I.104, G.106, V.107 No protein-ligand interaction detected (PLIP)

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

NAG.28: 6 residues within 4Å: Chain A: N.102, R.112, G.113, K.116, R.139, K.158 Ligand excluded by PLIP NAG.29: 4 residues within 4Å: Chain A: N.121, K.130, Q.131, K.132 Ligand excluded by PLIP NAG.30: 6 residues within 4Å: Chain A: E.244, N.245, T.247 Chain B: Q.167, S.168, Y.229 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain A: K.303, N.307, W.363 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain A: N.354, S.356 Ligands: NAG.33, NAG.35 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: N.360 Ligands: NAG.32, NAG.35 Ligand excluded by PLIP NAG.34: 2 residues within 4Å: Chain A: P.260, N.415 Ligand excluded by PLIP NAG.35: 6 residues within 4Å: Chain A: N.331, S.332, T.340, S.356 Ligands: NAG.32, NAG.33 Ligand excluded by PLIP NAG.36: 6 residues within 4Å: Chain C: N.102, R.112, G.113, K.116, R.139, K.158 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain C: N.121, K.130, Q.131, K.132 Ligand excluded by PLIP NAG.38: 6 residues within 4Å: Chain C: E.244, N.245, T.247 Chain D: S.168, G.169, Y.229 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain C: K.303, N.307, W.363 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: N.354, S.356 Ligands: NAG.43 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.360 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: P.260, N.415 Ligand excluded by PLIP NAG.43: 6 residues within 4Å: Chain C: N.331, S.332, T.340, N.354, S.356 Ligands: NAG.40 Ligand excluded by PLIP NAG.44: 6 residues within 4Å: Chain E: N.102, R.112, G.113, K.116, R.139, K.158 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain E: N.121, K.130, Q.131, K.132 Ligand excluded by PLIP NAG.46: 6 residues within 4Å: Chain E: E.244, N.245, T.247 Chain F: S.168, G.169, Y.229 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain E: K.303, N.307, W.363 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain E: N.354, S.356 Ligands: NAG.49, NAG.51 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain E: N.360 Ligands: NAG.48, NAG.51 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain E: P.260, Q.262, N.415 Ligand excluded by PLIP NAG.51: 7 residues within 4Å: Chain E: N.331, S.332, T.340, N.354, S.356 Ligands: NAG.48, NAG.49 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain G: N.94, S.96, W.97 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain G: K.116, E.117, N.120 Ligand excluded by PLIP NAG.54: 5 residues within 4Å: Chain A: E.1 Chain G: N.99, R.100, N.101, L.102 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain L: N.94, S.96, W.97 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain L: E.117, N.120, Y.121 Ligand excluded by PLIP NAG.57: 4 residues within 4Å: Chain C: E.1 Chain L: N.101, L.102 Chain P: R.55 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain Q: N.94, S.96 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain Q: E.117, N.120, Y.121 Ligand excluded by PLIP NAG.60: 5 residues within 4Å: Chain E: E.1, L.3 Chain Q: N.99, R.100, N.101 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Torrents de la Pena, A. et al., Improving the Immunogenicity of Native-like HIV-1 Envelope Trimers by Hyperstabilization. Cell Rep (2017)

Release Date

2018-04-04

Peptides

Envelope glycoprotein gp160: ACE
bnAb NIH45-46 scFv: BDF
Envelope glycoprotein gp160: GLQ
bnAb PGT122 Fab light chain: HMR
bnAb PGT122 Fab heavy chain: INS
bnAb 35O22 Fab heavy chain: JOT
bnAb 35O22 Fab light chain: KPU

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

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F

E
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F
W

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R
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C

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Envelope glycoprotein gp160

bnAb NIH45-46 scFv

Envelope glycoprotein gp160

bnAb PGT122 Fab light chain

bnAb PGT122 Fab heavy chain

bnAb 35O22 Fab heavy chain

bnAb 35O22 Fab light chain

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