SMTL ID : 8tgo.1

Crystal structure of the BG505 triple tandem trimer gp140 HIV-1 Env in complex with PGT124 and 35O22

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 5.75 Å

Oligo State

hetero-3-3-3-3-3-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: 16 residues within 4Å: Chain A: S.17 Chain B: N.30, F.31, Y.32, H.33, W.50, S.52, Y.54, D.57, R.110, D.111, G.112, S.113, T.115, H.249 Chain D: N.58 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.115, B:T.115, B:D.57, B:D.57, B:D.57, B:H.33, B:S.52, B:T.115

14 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: 2 residues within 4Å: Chain B: N.69, E.90 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain D: N.265, N.301, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 4 residues within 4Å: Chain D: N.271, T.273, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain D: N.232, L.235, P.261, N.416 Ligands: NAG-NAG-BMA.4 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain D: R.278 Chain I: R.162, N.167, T.168 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain I: C.101, T.102, N.103, R.113 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 1 residues within 4Å: Chain G: N.69 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 2 residues within 4Å: Chain I: N.265, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 4 residues within 4Å: Chain I: N.271, T.273, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 5 residues within 4Å: Chain I: N.232, L.235, P.261, N.416 Ligands: NAG-NAG-BMA.14 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 2 residues within 4Å: Chain L: N.69, R.92 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 6 residues within 4Å: Chain N: N.265, N.301, V.302, S.303, S.381, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain N: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 5 residues within 4Å: Chain N: N.232, L.235, P.261, N.416 Ligands: NAG-NAG-BMA.22 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.3: 5 residues within 4Å: Chain D: V.104, N.118, S.120, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.4: 11 residues within 4Å: Chain D: E.181, P.182, V.224, L.231, N.232, N.346, G.348, C.413, V.414, S.415 Ligands: NAG-NAG.8 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:G.348 NAG-NAG-BMA.13: 5 residues within 4Å: Chain I: V.104, N.118, S.120, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 7 residues within 4Å: Chain I: E.181, P.182, L.231, N.232, G.348, S.415 Ligands: NAG-NAG.18 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:G.348 NAG-NAG-BMA.21: 3 residues within 4Å: Chain N: V.104, N.118, Y.135 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:Y.135 NAG-NAG-BMA.22: 10 residues within 4Å: Chain N: E.181, L.231, N.232, F.345, G.348, R.412, C.413, V.414, S.415 Ligands: NAG-NAG.26 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.7: 19 residues within 4Å: Chain C: S.25, Q.47, P.61, D.62, I.63 Chain D: T.267, R.296, H.299, N.301, S.381, R.412 Chain E: G.101, Q.102, R.103, I.104, Y.105, G.106, V.107, V.108 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:R.296, D:R.296, E:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.17: 18 residues within 4Å: Chain H: S.25, Q.47, P.61, D.62, I.63 Chain I: T.267, R.296, H.299, N.301, R.412 Chain J: G.101, Q.102, R.103, I.104, G.106, V.107, V.108, Y.116 3 PLIP interactions: 1 interactions with chain J, 2 interactions with chain I Hydrogen bonds: J:V.108, I:R.296, I:R.296 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN.25: 20 residues within 4Å: Chain M: S.25, R.26, N.45, Q.47, P.61, D.62, I.63 Chain N: T.267, R.296, H.299, N.301, S.381, R.412 Chain O: G.101, Q.102, R.103, I.104, G.106, V.107, V.108 3 PLIP interactions: 1 interactions with chain O, 2 interactions with chain N Hydrogen bonds: O:V.108, N:R.296, N:R.296

2 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.10: 12 residues within 4Å: Chain F: S.17 Chain G: N.30, F.31, H.33, S.52, Y.54, R.110, G.112, S.113, T.115, H.249 Chain I: N.58 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:T.115, G:T.115, G:G.112, G:R.110, G:R.110 Hydrophobic interactions: G:R.110 NAG-NAG-BMA-MAN.19: 15 residues within 4Å: Chain K: S.17 Chain L: N.30, F.31, Y.32, H.33, S.52, Y.54, R.110, D.111, G.112, S.113, T.115, W.116, H.249 Chain N: N.58 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:G.112, L:T.115, L:W.116, L:H.249, L:H.33, L:T.115

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

NAG.27: 2 residues within 4Å: Chain A: N.100, S.102 Ligand excluded by PLIP NAG.28: 8 residues within 4Å: Chain A: R.106, E.110, N.114, M.115, Q.119 Chain B: Q.1, Y.32, Y.119 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain A: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain D: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.31: 2 residues within 4Å: Chain D: N.167 Chain N: R.278 Ligand excluded by PLIP NAG.32: 5 residues within 4Å: Chain D: N.204, T.206, S.244, E.245, I.247 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain D: N.246, T.248, N.249 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain D: N.324 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain D: N.355, S.357 Ligands: NAG.36 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain D: G.358, N.361 Ligands: NAG.35 Ligand excluded by PLIP NAG.37: 6 residues within 4Å: Chain D: C.101, T.102, N.103, D.110, R.113, K.117 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain F: N.100 Ligand excluded by PLIP NAG.39: 9 residues within 4Å: Chain F: R.106, D.113, N.114 Chain G: Q.1, Y.32, K.106, L.108, L.109, R.110 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain F: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.41: 4 residues within 4Å: Chain I: Q.100, S.120, F.121, N.122 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain I: N.204, S.244, E.245, I.247 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain I: N.246, T.248, N.249 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain I: N.324 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain I: N.355, S.357 Ligands: NAG.46 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain I: G.358, N.361 Ligands: NAG.45 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain K: N.100, S.102 Ligand excluded by PLIP NAG.48: 10 residues within 4Å: Chain K: R.106, E.110, D.113, N.114 Chain L: Q.1, Y.32, K.106, L.108, L.109, R.110 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain K: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.50: 5 residues within 4Å: Chain N: Q.100, S.120, F.121, N.122, K.133 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain N: N.167 Ligand excluded by PLIP NAG.52: 5 residues within 4Å: Chain N: N.204, T.206, S.244, E.245, I.247 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain N: N.246, T.248, N.249 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain N: N.324 Ligand excluded by PLIP NAG.55: 3 residues within 4Å: Chain N: N.355, S.357 Ligands: NAG.56 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain N: N.361 Ligands: NAG.55 Ligand excluded by PLIP NAG.57: 6 residues within 4Å: Chain N: C.101, T.102, N.103, D.110, R.113, K.117 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Del Moral-Sanchez, I. et al., Triple tandem trimer immunogens for HIV-1 and influenza nucleic acid-based vaccines. Npj Vaccines (2024)

Release Date

2024-04-17

Peptides

Envelope glycoprotein gp41: AFK
35O22 scFv: BGL
PGT124 light chain: CHM
Envelope glycoprotein gp120: DIN
PGT124 heavy chain: EJO

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

F
H

K
a

B
D

G
L

L
b

C
C

H
P

M
c

D
G

I
R

N
e

E
O

J
S

O
f

Envelope glycoprotein gp41

35O22 scFv

PGT124 light chain

Envelope glycoprotein gp120

PGT124 heavy chain

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