SMTL ID : 6w03.1

Crystal Structure of HIV-1 BG505 DS-SOSIP.3mut Prefusion Env Trimer in Complex with Human Antibodies 3H109L and 35O22 at 3.3 Angstrom

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

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

Ligands

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.1: 10 residues within 4Å: Chain D: E.181, P.182, L.231, N.232, N.346, G.348, C.413, V.414, S.415 Ligands: NAG-NAG.2 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.348 NAG-NAG-BMA-MAN.17: 10 residues within 4Å: Chain J: E.181, P.182, L.231, N.232, N.346, G.348, C.413, V.414, S.415 Ligands: NAG-NAG.18 1 PLIP interactions: 1 interactions with chain J Hydrogen bonds: J:G.348 NAG-NAG-BMA-MAN.33: 10 residues within 4Å: Chain P: E.181, P.182, L.231, N.232, N.346, G.348, C.413, V.414, S.415 Ligands: NAG-NAG.34 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:G.348

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: K.222, N.232, L.235, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.1 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 6 residues within 4Å: Chain D: Q.263, N.265, N.301, V.302, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain D: N.204, T.206, S.244, E.245, I.247 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain D: V.144, R.162, I.164, N.167 Chain J: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain D: C.101, T.102, N.103 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 6 residues within 4Å: Chain J: K.222, N.232, L.235, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.17 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 6 residues within 4Å: Chain J: Q.263, N.265, N.301, V.302, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 5 residues within 4Å: Chain J: N.204, T.206, S.244, E.245, I.247 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 5 residues within 4Å: Chain J: V.144, R.162, I.164, N.167 Chain P: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain J: C.101, T.102, N.103 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 6 residues within 4Å: Chain P: K.222, N.232, L.235, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.33 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 6 residues within 4Å: Chain P: Q.263, N.265, N.301, V.302, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 5 residues within 4Å: Chain P: N.204, T.206, S.244, E.245, I.247 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 5 residues within 4Å: Chain D: R.278 Chain P: V.144, R.162, I.164, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 3 residues within 4Å: Chain P: C.101, T.102, N.103 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: 2 residues within 4Å: Chain D: N.118, Y.135 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.23: 2 residues within 4Å: Chain J: N.118, Y.135 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.39: 2 residues within 4Å: Chain P: N.118, Y.135 No protein-ligand interaction detected (PLIP)

3 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.8: 3 residues within 4Å: Chain D: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.24: 3 residues within 4Å: Chain J: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.40: 3 residues within 4Å: Chain P: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP)

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.9: 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: E.57, N.58 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:T.115, C:H.96, B:D.111, B:S.113, B:H.33, B:S.52, B:S.52 Hydrophobic interactions: B:T.115 NAG-NAG-BMA-MAN-MAN-MAN.25: 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: E.57, N.58 5 PLIP interactions: 4 interactions with chain H, 1 interactions with chain I Hydrogen bonds: H:T.115, I:H.96, H:D.111, H:S.113, H:H.33, H:S.52, H:S.52 Hydrophobic interactions: H:T.115 NAG-NAG-BMA-MAN-MAN-MAN.41: 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: E.57, N.58 5 PLIP interactions: 1 interactions with chain O, 4 interactions with chain N Hydrogen bonds: O:H.96, N:T.115, N:D.111, N:S.113, N:H.33, N:S.52, N:S.52 Hydrophobic interactions: N:T.115

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.10: 21 residues within 4Å: Chain D: T.267, R.296, H.299, N.301, T.383, R.412 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 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D Hydrogen bonds: E:V.108, D:R.296, D:R.296 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.26: 21 residues within 4Å: Chain J: T.267, R.296, H.299, N.301, T.383, R.412 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 3 PLIP interactions: 2 interactions with chain J, 1 interactions with chain K Hydrogen bonds: J:R.296, J:R.296, K:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.42: 21 residues within 4Å: Chain P: T.267, R.296, H.299, N.301, T.383, R.412 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 3 PLIP interactions: 2 interactions with chain P, 1 interactions with chain Q Hydrogen bonds: P:R.296, P:R.296, Q:V.108

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

NAG.11: 3 residues within 4Å: Chain A: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.12: 2 residues within 4Å: Chain A: N.100, S.102 Ligand excluded by PLIP NAG.13: 5 residues within 4Å: Chain D: Q.100, S.120, F.121, N.122, K.133 Ligand excluded by PLIP NAG.14: 3 residues within 4Å: Chain D: N.246, T.248, N.249 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain D: N.355, S.357 Ligands: NAG.16 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain D: N.332, N.355 Ligands: NAG.15 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain G: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.28: 2 residues within 4Å: Chain G: N.100, S.102 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain J: Q.100, S.120, F.121, N.122, K.133 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain J: N.246, T.248, N.249 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain J: N.355, S.357 Ligands: NAG.32 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain J: N.332, N.355 Ligands: NAG.31 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain M: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.44: 2 residues within 4Å: Chain M: N.100, S.102 Ligand excluded by PLIP NAG.45: 5 residues within 4Å: Chain P: Q.100, S.120, F.121, N.122, K.133 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain P: N.246, T.248, N.249 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain P: N.355, S.357 Ligands: NAG.48 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain P: N.332, N.355 Ligands: NAG.47 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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