SMTL ID : 5utf.1

Crystal Structure of a Stabilized DS-SOSIP.6mut BG505 gp140 HIV-1 Env Trimer, Containing Mutations I201C-P433C (DS), L154M, Y177W, N300M, N302M, T320L, I420M in Complex with Human Antibodies PGT122 and 35O22 at 4.3 A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.50 Å

Oligo State

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

Ligands

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.1: 22 residues within 4Å: Chain A: N.58 Chain B: L.9, G.16, S.17 Chain E: N.30, F.31, H.33, W.50, S.52, Y.54, D.57, K.58, N.59, L.60, R.110, D.111, G.112, T.115 Chain F: H.95, N.96, S.97, G.98 6 PLIP interactions: 1 interactions with chain F, 5 interactions with chain E Hydrogen bonds: F:H.95, E:T.115, E:H.33, E:S.52, E:S.52, E:D.111 Hydrophobic interactions: E:R.110 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.22: 22 residues within 4Å: Chain G: N.58 Chain H: L.9, G.16, S.17 Chain K: N.30, F.31, H.33, W.50, S.52, Y.54, D.57, K.58, N.59, L.60, R.110, D.111, G.112, T.115 Chain L: H.95, N.96, S.97, G.98 6 PLIP interactions: 5 interactions with chain K, 1 interactions with chain L Hydrogen bonds: K:T.115, L:H.95, K:H.33, K:S.52, K:S.52, K:D.111 Hydrophobic interactions: K:R.110 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.43: 22 residues within 4Å: Chain M: N.58 Chain N: L.9, G.16, S.17 Chain Q: N.30, F.31, H.33, W.50, S.52, Y.54, D.57, K.58, N.59, L.60, R.110, D.111, G.112, T.115 Chain R: H.95, N.96, S.97, G.98 6 PLIP interactions: 5 interactions with chain Q, 1 interactions with chain R Hydrogen bonds: Q:T.115, R:H.95, Q:H.33, Q:S.52, Q:S.52, Q:D.111 Hydrophobic interactions: Q:R.110

3 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: 7 residues within 4Å: Chain A: N.107 Chain C: W.88, D.89, R.92, T.94 Chain D: N.58, T.115 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.58, D:T.115, D:T.115 NAG-NAG-BMA.23: 7 residues within 4Å: Chain G: N.107 Chain I: W.88, D.89, R.92, T.94 Chain J: N.58, T.115 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:N.58, J:T.115, J:T.115 NAG-NAG-BMA.44: 7 residues within 4Å: Chain M: N.107 Chain O: W.88, D.89, R.92, T.94 Chain P: N.58, T.115 3 PLIP interactions: 3 interactions with chain P Hydrogen bonds: P:N.58, P:T.115, P:T.115

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

NAG-NAG.3: 5 residues within 4Å: Chain A: N.204, T.206, S.244, I.247 Chain E: P.77 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 7 residues within 4Å: Chain A: N.332, S.333, N.355, S.357 Ligands: NAG-NAG.6, NAG-NAG.6, NAG-NAG.7 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG-NAG.5, NAG-NAG.5, NAG-NAG.7 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain A: N.361 Ligands: NAG-NAG.5, NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain A: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.4 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 4 residues within 4Å: Chain A: T.98, Q.100, N.122, K.131 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain A: V.144, R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain A: N.265, N.301, V.302, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 2 residues within 4Å: Chain A: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 5 residues within 4Å: Chain G: N.204, T.206, S.244, I.247 Chain K: P.77 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 7 residues within 4Å: Chain G: N.332, S.333, N.355, S.357 Ligands: NAG-NAG.27, NAG-NAG.27, NAG-NAG.28 No protein-ligand interaction detected (PLIP) NAG-NAG.27: 5 residues within 4Å: Chain G: N.355, S.357 Ligands: NAG-NAG.26, NAG-NAG.26, NAG-NAG.28 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 3 residues within 4Å: Chain G: N.361 Ligands: NAG-NAG.26, NAG-NAG.27 No protein-ligand interaction detected (PLIP) NAG-NAG.29: 4 residues within 4Å: Chain G: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.25 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 4 residues within 4Å: Chain G: T.98, Q.100, N.122, K.131 No protein-ligand interaction detected (PLIP) NAG-NAG.32: 3 residues within 4Å: Chain G: V.144, R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 5 residues within 4Å: Chain G: N.265, N.301, V.302, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.34: 2 residues within 4Å: Chain G: N.271, I.292 No protein-ligand interaction detected (PLIP) NAG-NAG.45: 5 residues within 4Å: Chain M: N.204, T.206, S.244, I.247 Chain Q: P.77 No protein-ligand interaction detected (PLIP) NAG-NAG.47: 7 residues within 4Å: Chain M: N.332, S.333, N.355, S.357 Ligands: NAG-NAG.48, NAG-NAG.48, NAG-NAG.49 No protein-ligand interaction detected (PLIP) NAG-NAG.48: 5 residues within 4Å: Chain M: N.355, S.357 Ligands: NAG-NAG.47, NAG-NAG.47, NAG-NAG.49 No protein-ligand interaction detected (PLIP) NAG-NAG.49: 3 residues within 4Å: Chain M: N.361 Ligands: NAG-NAG.47, NAG-NAG.48 No protein-ligand interaction detected (PLIP) NAG-NAG.50: 4 residues within 4Å: Chain M: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.46 No protein-ligand interaction detected (PLIP) NAG-NAG.52: 4 residues within 4Å: Chain M: T.98, Q.100, N.122, K.131 No protein-ligand interaction detected (PLIP) NAG-NAG.53: 3 residues within 4Å: Chain M: V.144, R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.54: 5 residues within 4Å: Chain M: N.265, N.301, V.302, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.55: 2 residues within 4Å: Chain M: N.271, I.292 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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.4: 14 residues within 4Å: Chain A: K.35, S.179, E.181, L.231, N.232, N.346, C.347, G.348, Q.408, R.412, C.413, V.414, S.415 Ligands: NAG-NAG.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.348 NAG-NAG-BMA-MAN-MAN-MAN.25: 14 residues within 4Å: Chain G: K.35, S.179, E.181, L.231, N.232, N.346, C.347, G.348, Q.408, R.412, C.413, V.414, S.415 Ligands: NAG-NAG.29 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:G.348 NAG-NAG-BMA-MAN-MAN-MAN.46: 14 residues within 4Å: Chain M: K.35, S.179, E.181, L.231, N.232, N.346, C.347, G.348, Q.408, R.412, C.413, V.414, S.415 Ligands: NAG-NAG.50 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:G.348

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.9: 4 residues within 4Å: Chain A: T.105, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.30: 4 residues within 4Å: Chain G: T.105, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.51: 4 residues within 4Å: Chain M: T.105, N.118, Y.135, D.290 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-(1-3)-[alpha-D-mannopyranose-(1-6)]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.14: 18 residues within 4Å: Chain A: T.267, H.299, N.301, S.381, T.383 Chain C: S.24, N.44, N.45, N.46, P.60, G.61, S.62 Chain D: R.103, I.104, Y.105, G.106, V.107, V.108 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:V.108 Hydrogen bonds: D:V.107 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.35: 18 residues within 4Å: Chain G: T.267, H.299, N.301, S.381, T.383 Chain I: S.24, N.44, N.45, N.46, P.60, G.61, S.62 Chain J: R.103, I.104, Y.105, G.106, V.107, V.108 2 PLIP interactions: 2 interactions with chain J Hydrophobic interactions: J:V.108 Hydrogen bonds: J:V.107 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.56: 18 residues within 4Å: Chain M: T.267, H.299, N.301, S.381, T.383 Chain O: S.24, N.44, N.45, N.46, P.60, G.61, S.62 Chain P: R.103, I.104, Y.105, G.106, V.107, V.108 2 PLIP interactions: 2 interactions with chain P Hydrophobic interactions: P:V.108 Hydrogen bonds: P:V.107

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

NAG.15: 3 residues within 4Å: Chain A: N.246, T.248, N.249 Ligand excluded by PLIP NAG.16: 2 residues within 4Å: Chain A: N.308, W.364 Ligand excluded by PLIP NAG.17: 1 residues within 4Å: Chain A: N.324 Ligand excluded by PLIP NAG.18: 5 residues within 4Å: Chain A: C.101, T.102, N.103, G.114, K.117 Ligand excluded by PLIP NAG.19: 2 residues within 4Å: Chain B: N.100, S.102 Ligand excluded by PLIP NAG.20: 4 residues within 4Å: Chain B: N.107 Chain F: N.54, E.55, R.56 Ligand excluded by PLIP NAG.21: 2 residues within 4Å: Chain B: E.123, N.126 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain G: N.246, T.248, N.249 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain G: N.308, W.364 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain G: N.324 Ligand excluded by PLIP NAG.39: 5 residues within 4Å: Chain G: C.101, T.102, N.103, G.114, K.117 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain H: N.100, S.102 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain H: N.107 Chain L: N.54, E.55, R.56 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain H: E.123, N.126 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain M: N.246, T.248, N.249 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain M: N.308, W.364 Ligand excluded by PLIP NAG.59: 1 residues within 4Å: Chain M: N.324 Ligand excluded by PLIP NAG.60: 5 residues within 4Å: Chain M: C.101, T.102, N.103, G.114, K.117 Ligand excluded by PLIP NAG.61: 2 residues within 4Å: Chain N: N.100, S.102 Ligand excluded by PLIP NAG.62: 4 residues within 4Å: Chain N: N.107 Chain R: N.54, E.55, R.56 Ligand excluded by PLIP NAG.63: 2 residues within 4Å: Chain N: E.123, N.126 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chuang, G.Y. et al., Structure-Based Design of a Soluble Prefusion-Closed HIV-1 Env Trimer with Reduced CD4 Affinity and Improved Immunogenicity. J. Virol. (2017)

Release Date

2017-03-29

Peptides

Envelope glycoprotein gp120: AGM
Envelope glycoprotein gp41: BHN
PGT122 Light chain: CIO
PGT122 Heavy chain: DJP
35022 Heavy chain: EKQ
35022 Light Chain: FLR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
G

G
G

M
G

B
B

H
B

N
B

C
L

I
L

O
L

D
H

J
H

P
H

E
D

K
D

Q
D

F
E

L
E

R
E

Envelope glycoprotein gp120

Envelope glycoprotein gp41

PGT122 Light chain

PGT122 Heavy chain

35022 Heavy chain

35022 Light Chain

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