SMTL ID : 6vzi.1

Crystal Structure of HIV-1 CAP256 RnS-3mut-2G-SOSIP.664 Prefusion Env Trimer in Complex with Human Antibodies 3H109L and 35O22 at 3.5 Angstrom

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.72 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: 17 residues within 4Å: Chain A: S.18 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: E.55, N.56 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:N.97, B:T.115, B:T.115, B:S.113, B:H.33, B:S.52, B:T.115 NAG-NAG-BMA-MAN-MAN-MAN.16: 17 residues within 4Å: Chain G: S.18 Chain H: 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 I: H.96, N.97 Chain J: E.55, N.56 4 PLIP interactions: 1 interactions with chain I, 3 interactions with chain H Hydrogen bonds: I:N.97, H:T.115, H:T.115, H:S.113, H:H.33, H:S.52, H:T.115 NAG-NAG-BMA-MAN-MAN-MAN.31: 17 residues within 4Å: Chain M: S.18 Chain N: 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 O: H.96, N.97 Chain P: E.55, N.56 4 PLIP interactions: 3 interactions with chain N, 1 interactions with chain O Hydrogen bonds: N:T.115, N:T.115, O:N.97, N:S.113, N:H.33, N:S.52, N:T.115

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.2: 5 residues within 4Å: Chain D: N.117, S.119, R.132, Y.134, D.284 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 11 residues within 4Å: Chain D: D.175, P.176, L.225, N.226, F.337, N.338, G.340, C.403, K.404, S.405 Ligands: NAG-NAG.6 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.340 NAG-NAG-BMA.17: 5 residues within 4Å: Chain J: N.117, S.119, R.132, Y.134, D.284 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.18: 11 residues within 4Å: Chain J: D.175, P.176, L.225, N.226, F.337, N.338, G.340, C.403, K.404, S.405 Ligands: NAG-NAG.21 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:G.340 NAG-NAG-BMA.32: 5 residues within 4Å: Chain P: N.117, S.119, R.132, Y.134, D.284 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.33: 11 residues within 4Å: Chain P: D.175, P.176, L.225, N.226, F.337, N.338, G.340, C.403, K.404, S.405 Ligands: NAG-NAG.36 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:G.340

9 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: 4 residues within 4Å: Chain D: N.265, T.267, I.286 Chain F: F.68 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain D: N.226, S.255, N.406 Ligands: NAG-NAG-BMA.3 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain D: E.51, N.193, N.205, S.207 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 4 residues within 4Å: Chain J: N.265, T.267, I.286 Chain L: F.68 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 4 residues within 4Å: Chain J: N.226, S.255, N.406 Ligands: NAG-NAG-BMA.18 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 4 residues within 4Å: Chain J: E.51, N.193, N.205, S.207 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 4 residues within 4Å: Chain P: N.265, T.267, I.286 Chain R: F.68 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 4 residues within 4Å: Chain P: N.226, S.255, N.406 Ligands: NAG-NAG-BMA.33 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 4 residues within 4Å: Chain P: E.51, N.193, N.205, S.207 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.5: 20 residues within 4Å: Chain D: T.261, R.290, H.293, N.295, T.373 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 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D Hydrogen bonds: E:V.108, D:R.290 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.20: 20 residues within 4Å: Chain J: T.261, R.290, H.293, N.295, T.373 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 2 PLIP interactions: 1 interactions with chain K, 1 interactions with chain J Hydrogen bonds: K:V.108, J:R.290 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.35: 20 residues within 4Å: Chain P: T.261, R.290, H.293, N.295, T.373 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 2 PLIP interactions: 1 interactions with chain P, 1 interactions with chain Q Hydrogen bonds: P:R.290, Q:V.108

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

NAG.8: 4 residues within 4Å: Chain D: S.119, F.120, N.121 Ligands: NAG.14 Ligand excluded by PLIP NAG.9: 2 residues within 4Å: Chain D: R.156, N.161 Ligand excluded by PLIP NAG.10: 7 residues within 4Å: Chain D: N.198, T.200, P.202, S.238, E.239, L.241, H.315 Ligand excluded by PLIP NAG.11: 3 residues within 4Å: Chain D: N.347, S.349, D.350 Ligand excluded by PLIP NAG.12: 5 residues within 4Å: Chain D: E.233, I.234, N.253, R.307, K.311 Ligand excluded by PLIP NAG.13: 4 residues within 4Å: Chain D: N.323, Q.324, F.353, R.427 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain D: N.98, E.154 Ligands: NAG.8 Ligand excluded by PLIP NAG.15: 2 residues within 4Å: Chain D: N.194, N.204 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain J: S.119, F.120, N.121 Ligands: NAG.29 Ligand excluded by PLIP NAG.24: 2 residues within 4Å: Chain J: R.156, N.161 Ligand excluded by PLIP NAG.25: 7 residues within 4Å: Chain J: N.198, T.200, P.202, S.238, E.239, L.241, H.315 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain J: N.347, S.349, D.350 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain J: E.233, I.234, N.253, R.307, K.311 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain J: N.323, Q.324, F.353, R.427 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain J: N.98, E.154 Ligands: NAG.23 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain J: N.194, N.204 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain P: S.119, F.120, N.121 Ligands: NAG.44 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain P: R.156, N.161 Ligand excluded by PLIP NAG.40: 7 residues within 4Å: Chain P: N.198, T.200, P.202, S.238, E.239, L.241, H.315 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain P: N.347, S.349, D.350 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain P: E.233, I.234, N.253, R.307, K.311 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain P: N.323, Q.324, F.353, R.427 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain P: N.98, E.154 Ligands: NAG.38 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain P: N.194, N.204 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chuang, G.Y. et al., Development of a 3Mut-Apex-Stabilized Envelope Trimer That Expands HIV-1 Neutralization Breadth When Used To Boost Fusion Peptide-Directed Vaccine-Elicited Responses. J.Virol. (2020)

Release Date

2020-04-15

Peptides

Envelope glycoprotein gp41: AGM
35O22 scFv heavy chain: BHN
35O22 scFv light chain: CIO
Envelope glycoprotein gp160: 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 gp160

3H109L Fab heavy chain

3H109L Fab light chain

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