SMTL ID : 6wix.1

Crystal Structure of HIV-1 MI369 RnS-DS.SOSIP Prefusion Env Trimer in Complex with Human Antibodies 3H109L and 35O22 at 3.5 Angstrom

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.67 Å

Oligo State

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

Ligands

3 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.1: 20 residues within 4Å: Chain A: S.17 Chain B: N.30, F.31, Y.32, H.33, W.50, S.52, Y.54, S.55, D.57, N.59, R.110, D.111, G.112, S.113, T.115 Chain C: H.96, N.97 Chain D: D.59, N.60 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.115, B:T.115, B:D.111, B:G.112, B:S.113, B:H.33, B:S.52, B:S.52, B:T.115 Hydrophobic interactions: B:R.110, B:T.115 NAG-NAG-BMA-MAN-MAN-MAN.15: 20 residues within 4Å: Chain G: S.17 Chain H: N.30, F.31, Y.32, H.33, W.50, S.52, Y.54, S.55, D.57, N.59, R.110, D.111, G.112, S.113, T.115 Chain I: H.96, N.97 Chain J: D.59, N.60 6 PLIP interactions: 6 interactions with chain H Hydrogen bonds: H:T.115, H:T.115, H:D.111, H:G.112, H:S.113, H:H.33, H:S.52, H:S.52, H:T.115 Hydrophobic interactions: H:R.110, H:T.115 NAG-NAG-BMA-MAN-MAN-MAN.29: 20 residues within 4Å: Chain M: S.17 Chain N: N.30, F.31, Y.32, H.33, W.50, S.52, Y.54, S.55, D.57, N.59, R.110, D.111, G.112, S.113, T.115 Chain O: H.96, N.97 Chain P: D.59, N.60 6 PLIP interactions: 6 interactions with chain N Hydrogen bonds: N:T.115, N:T.115, N:D.111, N:G.112, N:S.113, N:H.33, N:S.52, N:S.52, N:T.115 Hydrophobic interactions: N:R.110, N:T.115

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

NAG-NAG.2: 6 residues within 4Å: Chain D: F.106, N.136, S.138, R.151, H.153, A.305 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 1 residues within 4Å: Chain D: N.182 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain D: N.286, T.288, I.307, V.427 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain D: N.369, S.371 Ligands: NAG.14 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain D: N.247, P.276, N.433 Ligands: NAG-NAG-BMA.4 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 6 residues within 4Å: Chain J: F.106, N.136, S.138, R.151, H.153, A.305 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 1 residues within 4Å: Chain J: N.182 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain J: N.286, T.288, I.307, V.427 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain J: N.369, S.371 Ligands: NAG.28 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 4 residues within 4Å: Chain J: N.247, P.276, N.433 Ligands: NAG-NAG-BMA.18 No protein-ligand interaction detected (PLIP) NAG-NAG.30: 6 residues within 4Å: Chain P: F.106, N.136, S.138, R.151, H.153, A.305 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 1 residues within 4Å: Chain P: N.182 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 4 residues within 4Å: Chain P: N.286, T.288, I.307, V.427 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 3 residues within 4Å: Chain P: N.369, S.371 Ligands: NAG.42 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 4 residues within 4Å: Chain P: N.247, P.276, N.433 Ligands: NAG-NAG-BMA.32 No protein-ligand interaction detected (PLIP)

6 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.4: 11 residues within 4Å: Chain D: E.196, P.197, L.246, N.247, F.359, N.360, G.362, C.430, V.431, S.432 Ligands: NAG-NAG.10 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.362 NAG-NAG-BMA.9: 6 residues within 4Å: Chain D: N.280, V.431 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.6, NAG-NAG-NAG.8, NAG-NAG-NAG.8, NAG-NAG-NAG.8 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 11 residues within 4Å: Chain J: E.196, P.197, L.246, N.247, F.359, N.360, G.362, C.430, V.431, S.432 Ligands: NAG-NAG.24 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:G.362 NAG-NAG-BMA.23: 6 residues within 4Å: Chain J: N.280, V.431 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.20, NAG-NAG-NAG.22, NAG-NAG-NAG.22, NAG-NAG-NAG.22 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.32: 11 residues within 4Å: Chain P: E.196, P.197, L.246, N.247, F.359, N.360, G.362, C.430, V.431, S.432 Ligands: NAG-NAG.38 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:G.362 NAG-NAG-BMA.37: 6 residues within 4Å: Chain P: N.280, V.431 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.34, NAG-NAG-NAG.36, NAG-NAG-NAG.36, NAG-NAG-NAG.36 No protein-ligand interaction detected (PLIP)

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.6: 23 residues within 4Å: Chain D: T.282, R.311, H.314, N.316, N.398, T.400 Chain E: Q.100, 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 Ligands: NAG-NAG-NAG.8, NAG-NAG-BMA.9 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:V.108, D:R.311, D:R.311 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.20: 23 residues within 4Å: Chain J: T.282, R.311, H.314, N.316, N.398, T.400 Chain K: Q.100, K.102, R.103, I.104, Y.105, G.106, M.107, V.108 Chain L: S.28, N.48, N.49, Q.50, P.64, D.65, I.66 Ligands: NAG-NAG-NAG.22, NAG-NAG-BMA.23 3 PLIP interactions: 1 interactions with chain K, 2 interactions with chain J Hydrogen bonds: K:V.108, J:R.311, J:R.311 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.34: 23 residues within 4Å: Chain P: T.282, R.311, H.314, N.316, N.398, T.400 Chain Q: Q.100, K.102, R.103, I.104, Y.105, G.106, M.107, V.108 Chain R: S.28, N.48, N.49, Q.50, P.64, D.65, I.66 Ligands: NAG-NAG-NAG.36, NAG-NAG-BMA.37 3 PLIP interactions: 1 interactions with chain Q, 2 interactions with chain P Hydrogen bonds: Q:V.108, P:R.311, P:R.311

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

NAG-NAG-NAG.8: 6 residues within 4Å: Chain D: N.280, N.316, N.398 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.6, NAG-NAG-BMA.9, NAG-NAG-BMA.9 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.22: 6 residues within 4Å: Chain J: N.280, N.316, N.398 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.20, NAG-NAG-BMA.23, NAG-NAG-BMA.23 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.36: 6 residues within 4Å: Chain P: N.280, N.316, N.398 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.34, NAG-NAG-BMA.37, NAG-NAG-BMA.37 No protein-ligand interaction detected (PLIP)

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

NAG.11: 6 residues within 4Å: Chain D: N.219, T.221, P.223, S.259, E.260, H.336 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.219, D:T.221, D:T.221 NAG.12: 3 residues within 4Å: Chain D: H.102, F.139, N.140 No protein-ligand interaction detected (PLIP) NAG.13: 1 residues within 4Å: Chain D: N.226 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.226 NAG.14: 4 residues within 4Å: Chain D: S.371, G.372, N.375 Ligands: NAG-NAG.7 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.375 NAG.25: 6 residues within 4Å: Chain J: N.219, T.221, P.223, S.259, E.260, H.336 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:N.219, J:T.221, J:T.221 NAG.26: 3 residues within 4Å: Chain J: H.102, F.139, N.140 No protein-ligand interaction detected (PLIP) NAG.27: 1 residues within 4Å: Chain J: N.226 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:N.226 NAG.28: 4 residues within 4Å: Chain J: S.371, G.372, N.375 Ligands: NAG-NAG.21 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:N.375 NAG.39: 6 residues within 4Å: Chain P: N.219, T.221, P.223, S.259, E.260, H.336 3 PLIP interactions: 3 interactions with chain P Hydrogen bonds: P:N.219, P:T.221, P:T.221 NAG.40: 3 residues within 4Å: Chain P: H.102, F.139, N.140 No protein-ligand interaction detected (PLIP) NAG.41: 1 residues within 4Å: Chain P: N.226 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:N.226 NAG.42: 4 residues within 4Å: Chain P: S.371, G.372, N.375 Ligands: NAG-NAG.35 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:N.375

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rawi, R. et al., Automated Design by Structure-Based Stabilization and Consensus Repair to Achieve Prefusion-Closed Envelope Trimers in a Wide Variety of HIV Strains. Cell Rep (2020)

Release Date

2020-11-25

Peptides

Envelope glycoprotein gp41: AGM
35O22 scFv heavy chain: BHN
35O22 scFv light chain: CIO
Envelope glycoprotein gp120: DJP
3H109L Fab heavy chain: EKQ
3H109L Fab light chain: FLR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

G
B

M
B

B
D

H
D

N
D

C
E

I
E

O
E

D
G

J
G

P
G

E
H

K
H

Q
H

F
L

L
L

R
L

Envelope glycoprotein gp41

35O22 scFv heavy chain

35O22 scFv light chain

Envelope glycoprotein gp120

3H109L Fab heavy chain

3H109L Fab light chain

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