SMTL ID : 6ck9.1

Crystal Structure of HIV-1 ConC_Base0 Prefusion Env Trimer in Complex with Human Antibody Fragment 3H109L and 35O22 variants at 3.5 Angstrom

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.71 Å

Oligo State

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

Ligands

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.1: 8 residues within 4Å: Chain D: D.173, P.174, N.224, N.337, R.339, K.396, S.397 Ligands: NAG-NAG.10 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:K.396 Hydrogen bonds: D:D.173

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.2: 17 residues within 4Å: Chain A: G.16, S.17 Chain B: N.30, F.31, H.33, S.52, Y.54, S.55, D.57, R.110, D.111, G.112, S.113, T.115 Chain C: H.96, N.97 Chain D: N.56 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:H.96, B:D.111, B:G.112, B:H.33, B:S.52, B:S.52 Hydrophobic interactions: B:R.110

1 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.3: 7 residues within 4Å: Chain D: V.102, N.118, S.120, Y.135, L.137, D.282 Chain F: R.95 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.4: 3 residues within 4Å: Chain D: V.144, R.154, N.159 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain D: N.257, N.293, I.294, S.295, K.396 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain D: N.263, I.284 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 3 residues within 4Å: Chain D: T.332, N.346, S.348 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain D: N.398 Ligands: NAG-NAG-BMA-MAN-MAN.1, NAG-NAG-BMA-MAN-MAN.1 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.5: 5 residues within 4Å: Chain D: N.192, T.194, F.195, P.200, N.202 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.8: 20 residues within 4Å: Chain D: T.259, R.288, H.291, N.293, T.363, T.365 Chain E: K.102, R.103, I.104, Y.105, G.106, M.107, V.108 Chain F: S.28, N.48, N.49, Q.50, P.64, D.65, I.66 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:R.288, E:V.108

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

NAG.11: 2 residues within 4Å: Chain A: N.100, S.102 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.102 NAG.12: 2 residues within 4Å: Chain A: R.122, N.126 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.126 NAG.13: 4 residues within 4Å: Chain D: N.196, T.198, S.236, E.237 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.196, D:T.198 NAG.14: 2 residues within 4Å: Chain D: N.98, E.152 No protein-ligand interaction detected (PLIP) NAG.15: 3 residues within 4Å: Chain D: N.122, K.131, K.133 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:K.131 NAG.16: 2 residues within 4Å: Chain D: K.193, N.203 No protein-ligand interaction detected (PLIP) NAG.17: 2 residues within 4Å: Chain D: N.238, T.240 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.238, D:T.240 NAG.18: 6 residues within 4Å: Chain D: E.230, E.231, I.232, N.251, E.252, R.305 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.305 NAG.19: 2 residues within 4Å: Chain D: N.392, T.394 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.392

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rutten, L. et al., A Universal Approach to Optimize the Folding and Stability of Prefusion-Closed HIV-1 Envelope Trimers. Cell Rep (2018)

Release Date

2018-04-25

Peptides

gp41 ectodomain of Envelope glycoprotein gp160: A
35O22 scFv heavy chain portion: B
35O22 scFv light chain portion: C
gp120 of Envelope glycoprotein gp160: D
3H109L Fab heavy chain: E
3H109L Fab light chain: F

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
D

C
E

D
G

E
H

F
L

gp41 ectodomain of Envelope glycoprotein gp160

35O22 scFv heavy chain portion

35O22 scFv light chain portion

gp120 of Envelope glycoprotein gp160

3H109L Fab heavy chain

3H109L Fab light chain

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