SMTL ID : 6vrw.1

Cryo-EM structure of stabilized HIV-1 Env trimer CAP256.wk34.c80 SOSIP.RnS2

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-mer

Ligands

21 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: 3 residues within 4Å: Chain A: T.96, N.121, R.132 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 2 residues within 4Å: Chain A: N.98, E.154 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: R.156, N.161, T.162 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.194, T.196, P.202, N.204 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: E.51, N.193, N.205 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain A: T.259, T.261, H.293, N.295, T.371, T.373 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain A: E.232, E.233, I.234, N.253, R.307 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain C: T.96, N.121, R.132 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 2 residues within 4Å: Chain C: N.98, E.154 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain C: R.156, N.161, T.162 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain C: N.194, T.196, P.202, N.204 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain C: E.51, N.193, N.205 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 6 residues within 4Å: Chain C: T.259, T.261, H.293, N.295, T.371, T.373 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 5 residues within 4Å: Chain C: E.232, E.233, I.234, N.253, R.307 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 3 residues within 4Å: Chain E: T.96, N.121, R.132 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 2 residues within 4Å: Chain E: N.98, E.154 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 3 residues within 4Å: Chain E: R.156, N.161, T.162 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 4 residues within 4Å: Chain E: N.194, T.196, P.202, N.204 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain E: E.51, N.193, N.205 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 6 residues within 4Å: Chain E: T.259, T.261, H.293, N.295, T.371, T.373 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 5 residues within 4Å: Chain E: E.232, E.233, I.234, N.253, R.307 No protein-ligand interaction detected (PLIP)

3 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.7: 8 residues within 4Å: Chain A: T.173, D.175, V.218, N.226, N.338, G.340, K.404, S.405 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.175 NAG-NAG-BMA-MAN-MAN.15: 8 residues within 4Å: Chain C: T.173, D.175, V.218, N.226, N.338, G.340, K.404, S.405 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.175 NAG-NAG-BMA-MAN-MAN.23: 8 residues within 4Å: Chain E: T.173, D.175, V.218, N.226, N.338, G.340, K.404, S.405 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:D.175

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

NAG.25: 5 residues within 4Å: Chain A: N.117, S.119, Y.134, L.136, D.284 Ligand excluded by PLIP NAG.26: 4 residues within 4Å: Chain A: N.198, T.200, I.236, L.241 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain A: N.240, T.242, D.243 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain A: N.317 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain A: N.323, R.427 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain A: N.347, S.349, D.350, R.377 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain A: S.255, N.406 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain A: W.3, E.458, N.460 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain A: E.55, N.56 Chain B: S.18 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain A: P.263, N.265, N.400 Ligands: NAG.35 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain A: N.265, G.399 Ligands: NAG.34 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain B: N.101, S.103 Ligand excluded by PLIP NAG.37: 1 residues within 4Å: Chain B: N.127 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain C: N.117, S.119, Y.134, L.136, D.284 Ligand excluded by PLIP NAG.39: 4 residues within 4Å: Chain C: N.198, T.200, I.236, L.241 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain C: N.240, T.242, D.243 Ligand excluded by PLIP NAG.41: 1 residues within 4Å: Chain C: N.317 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: N.323, R.427 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain C: N.347, S.349, D.350, R.377 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain C: S.255, N.406 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain C: W.3, E.458, N.460 Chain D: N.97 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain C: E.55, N.56 Chain D: S.18 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain C: P.263, N.265, N.400 Ligands: NAG.48 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain C: N.265, G.399 Ligands: NAG.47 Ligand excluded by PLIP NAG.49: 2 residues within 4Å: Chain D: N.101, S.103 Ligand excluded by PLIP NAG.50: 1 residues within 4Å: Chain D: N.127 Ligand excluded by PLIP NAG.51: 5 residues within 4Å: Chain E: N.117, S.119, Y.134, L.136, D.284 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain E: N.198, T.200, I.236, L.241 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain E: N.240, T.242, D.243 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain E: N.317 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain E: N.323, R.427 Ligand excluded by PLIP NAG.56: 4 residues within 4Å: Chain E: N.347, S.349, D.350, R.377 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain E: S.255, N.406 Ligand excluded by PLIP NAG.58: 4 residues within 4Å: Chain E: W.3, E.458, N.460 Chain F: N.97 Ligand excluded by PLIP NAG.59: 3 residues within 4Å: Chain E: E.55, N.56 Chain F: S.18 Ligand excluded by PLIP NAG.60: 4 residues within 4Å: Chain E: P.263, N.265, N.400 Ligands: NAG.61 Ligand excluded by PLIP NAG.61: 3 residues within 4Å: Chain E: N.265, G.399 Ligands: NAG.60 Ligand excluded by PLIP NAG.62: 2 residues within 4Å: Chain F: N.101, S.103 Ligand excluded by PLIP NAG.63: 1 residues within 4Å: Chain F: N.127 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gorman, J. et al., Structure of Super-Potent Antibody CAP256-VRC26.25 in Complex with HIV-1 Envelope Reveals a Combined Mode of Trimer-Apex Recognition. Cell Rep (2020)

Release Date

2020-03-11

Peptides

Envelope glycoprotein gp120: ACE
Envelope glycoprotein gp41: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

C
A

E
D

B
B

D
C

F
E

Envelope glycoprotein gp120

Envelope glycoprotein gp41

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