SMTL ID : 9ogu.1

HIV-1 Env BG505 SOSIP.664-dPG-His in complex with PGT122 and 3BNC117 Fabs

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.20 Å

Oligo State

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

Ligands

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

NAG-NAG.1: 7 residues within 4Å: Chain A: V.139, T.140, N.153, Y.170, L.172, D.325 Chain J: R.89 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 6 residues within 4Å: Chain A: V.179, R.197, N.202 Chain F: R.313 Chain G: H.73, W.76 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 8 residues within 4Å: Chain A: N.367, S.368, T.376, N.390, S.392 Ligands: NAG-NAG.6, NAG-NAG.6, NAG.34 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 5 residues within 4Å: Chain A: N.390, S.392 Ligands: NAG-NAG.5, NAG-NAG.5, NAG.34 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 6 residues within 4Å: Chain E: V.139, T.140, N.153, S.155, Y.170 Chain N: R.89 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.170 NAG-NAG.10: 6 residues within 4Å: Chain E: V.179, R.197, N.202, T.203 Chain K: H.73, W.76 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain E: N.390 Ligands: NAG-NAG-BMA-MAN-MAN.14, NAG-NAG-BMA-MAN-MAN.14, NAG.46 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 7 residues within 4Å: Chain E: K.257, N.267, L.270, P.296, V.449, N.451 Ligands: NAG-NAG-BMA.11 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 6 residues within 4Å: Chain F: V.139, T.140, N.153, S.155, L.172, D.325 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 3 residues within 4Å: Chain F: N.306, T.308, I.327 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 6 residues within 4Å: Chain F: N.390, S.392 Ligands: NAG-NAG-BMA.24, NAG-NAG-BMA.24, NAG-NAG-BMA.24, NAG.52 No protein-ligand interaction detected (PLIP)

1 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.3: 9 residues within 4Å: Chain A: S.214, P.217, L.266, N.267, N.381, G.383, V.449, S.450 Ligands: NAG.35 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.383, A:S.214

1 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: 19 residues within 4Å: Chain A: N.300, T.302, D.329, R.331, H.334, N.336, T.418 Chain I: R.103, I.104, G.106, V.107, V.108 Chain J: S.22, N.42, N.43, P.58, G.59, S.60 Ligands: NAG.31 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.331

2 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.7: 11 residues within 4Å: Chain A: E.280, N.281, T.283 Chain H: N.26, G.27, Y.28, R.62, W.63, G.64, Y.67, Y.87 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:Y.28 Hydrogen bonds: H:R.62, H:R.62, H:G.64, H:G.64 NAG-NAG-BMA-MAN.19: 13 residues within 4Å: Chain F: S.214, E.216, P.217, K.257, V.259, L.266, N.267, N.381, R.447, C.448, V.449, S.450 Ligands: NAG.53 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:V.449 Hydrogen bonds: F:S.214

4 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.8: 13 residues within 4Å: Chain A: N.142 Chain I: Y.33, G.55, D.56, T.57, N.58, H.100, R.102, F.114, T.115 Chain J: W.86, D.87, T.92 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:N.58, I:T.115, I:T.115, I:T.57, I:N.58 NAG-NAG-BMA-MAN-MAN.14: 8 residues within 4Å: Chain E: D.146, N.367, S.368, T.376, N.390, S.392 Ligands: NAG-NAG.15, NAG-NAG.15 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.17: 12 residues within 4Å: Chain E: N.142, I.143 Chain M: Y.33, D.56, N.58, R.102, F.114 Chain N: W.86, D.87, S.88, R.90, T.92 2 PLIP interactions: 2 interactions with chain M Hydrogen bonds: M:N.58, M:T.115 NAG-NAG-BMA-MAN-MAN.26: 14 residues within 4Å: Chain F: N.142 Chain Q: Y.33, Y.50, H.52, G.55, D.56, T.57, H.100, F.114, T.115 Chain R: W.86, D.87, R.90, T.92 2 PLIP interactions: 2 interactions with chain Q Hydrogen bonds: Q:Y.50, Q:D.56, Q:Y.33, Q:H.52

4 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.11: 10 residues within 4Å: Chain E: E.216, P.217, V.259, L.266, N.267, N.381, G.383, V.449, S.450 Ligands: NAG-NAG.16 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:V.449 NAG-NAG-BMA.12: 6 residues within 4Å: Chain E: E.280, N.281 Chain L: G.27, Y.28, R.62, Y.87 1 PLIP interactions: 1 interactions with chain L Hydrophobic interactions: L:Y.28 Hydrogen bonds: L:R.62, L:G.64 NAG-NAG-BMA.20: 9 residues within 4Å: Chain F: E.280, N.281 Chain P: G.27, Y.28, R.62, Q.65, Y.67, Y.87 Ligands: NAG.50 1 PLIP interactions: 1 interactions with chain P Hydrophobic interactions: P:Y.28 Hydrogen bonds: P:R.62, P:Q.65 NAG-NAG-BMA.24: 6 residues within 4Å: Chain F: N.367, S.368, T.376, N.390 Ligands: NAG-NAG.25, NAG-NAG.25 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-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-MAN.13: 15 residues within 4Å: Chain E: T.302, H.334, N.336 Chain M: R.103, I.104, G.106, V.107, V.108 Chain N: S.22, N.42, N.43, N.44, P.58, G.59, S.60 1 PLIP interactions: 1 interactions with chain M Hydrogen bonds: M:G.106, M:V.108, M:R.103 NAG-NAG-BMA-MAN-MAN-MAN-MAN.23: 17 residues within 4Å: Chain F: N.300, T.302, R.331, H.334, N.336, R.447 Chain Q: R.103, I.104, G.106, V.107, V.108 Chain R: S.22, N.42, N.43, N.44, G.59, S.60 1 PLIP interactions: 1 interactions with chain Q Hydrogen bonds: Q:G.106, Q:V.108, Q:R.103

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

NAG-BMA.21: 4 residues within 4Å: Chain F: Q.298, N.300, S.338, R.447 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Q.298, F:R.447

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

NAG.27: 4 residues within 4Å: Chain A: E.92, N.93 Chain D: G.13, S.17 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain A: N.138 Ligand excluded by PLIP NAG.29: 5 residues within 4Å: Chain A: T.133, Q.135, S.155, F.156, N.157 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain A: N.239, T.241, G.242 Ligand excluded by PLIP NAG.31: 5 residues within 4Å: Chain A: Q.298, N.300, R.447, V.449 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.4 Ligand excluded by PLIP NAG.32: 2 residues within 4Å: Chain A: N.306, V.445 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain A: N.343, W.399 Ligand excluded by PLIP NAG.34: 5 residues within 4Å: Chain A: S.392, N.396 Ligands: NAG-NAG.5, NAG-NAG.6, NAG-NAG.6 Ligand excluded by PLIP NAG.35: 6 residues within 4Å: Chain A: N.267, L.270, P.296, V.449, N.451 Ligands: NAG-NAG-BMA-MAN.3 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain B: K.121, S.124, N.125, Y.126 Ligand excluded by PLIP NAG.37: 2 residues within 4Å: Chain C: N.125, Y.126 Ligand excluded by PLIP NAG.38: 5 residues within 4Å: Chain D: K.121, E.122, I.123, S.124, N.125 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain B: S.17 Chain E: E.92, N.93 Ligand excluded by PLIP NAG.40: 7 residues within 4Å: Chain E: C.136, N.138, R.148, K.152, N.193, K.194, Y.196 Ligand excluded by PLIP NAG.41: 6 residues within 4Å: Chain E: T.133, Q.135, S.155, F.156, N.157, K.168 Ligand excluded by PLIP NAG.42: 6 residues within 4Å: Chain E: D.235, K.237, F.238, N.239, T.241, P.243 Ligand excluded by PLIP NAG.43: 7 residues within 4Å: Chain E: Q.298, N.300, N.336, V.337, S.338, S.416, R.447 Ligand excluded by PLIP NAG.44: 3 residues within 4Å: Chain E: N.306, I.327, V.445 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain E: N.343, W.399 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain E: S.392, N.396 Ligands: NAG-NAG.15 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain F: N.138, R.148, G.149 Ligand excluded by PLIP NAG.48: 5 residues within 4Å: Chain F: Q.135, S.155, F.156, N.157, K.168 Ligand excluded by PLIP NAG.49: 7 residues within 4Å: Chain F: V.179, R.197, N.202, T.203 Chain O: H.73, A.74, W.76 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain F: N.239, T.241 Ligands: NAG-NAG-BMA.20 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain F: N.343, E.344, W.399 Ligand excluded by PLIP NAG.52: 5 residues within 4Å: Chain F: S.392, G.393, N.396 Ligands: NAG-NAG.25, NAG-NAG.25 Ligand excluded by PLIP NAG.53: 5 residues within 4Å: Chain F: L.270, P.296, V.449, N.451 Ligands: NAG-NAG-BMA-MAN.19 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain C: G.16, S.17 Chain F: E.92, N.93 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chaturbhuj, D.N. et al., A modification to heptad repeat 1 of gp41 improves yield and/or quality of soluble pre-fusion HIV-1 envelope glycoprotein trimers. J.Virol. (2025)

Release Date

2025-08-27

Peptides

HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp120: AEF
Envelope glycoprotein gp160: BCD
3BNC117 Fab heavy chain: GKO
3BNC117 Fab light chain: HLP
PGT122 Fab heavy chain: IMQ
PGT122 Fab light chain: JNR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
E

F
C

B
F

C
D

D
B

G
H

K
M

O
P

H
I

L
L

P
Q

I
J

M
N

Q
R

J
K

N
O

R
S

HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp120

Envelope glycoprotein gp160

3BNC117 Fab heavy chain

3BNC117 Fab light chain

PGT122 Fab heavy chain

PGT122 Fab light chain

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