SMTL ID : 9ogt.1

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

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.00 Å

Oligo State

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

Ligands

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.1: 6 residues within 4Å: Chain E: V.139, T.140, N.153, Y.170, L.172, D.325 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Y.170 NAG-NAG.4: 8 residues within 4Å: Chain B: N.26, G.27, Y.28, R.62, Y.87 Chain E: E.280, N.281 Ligands: NAG.31 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.28 Hydrogen bonds: B:R.62, B:R.62 NAG-NAG.6: 5 residues within 4Å: Chain E: N.390, S.392 Ligands: NAG-NAG-NAG.7, NAG-NAG-NAG.7, NAG.29 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 6 residues within 4Å: Chain K: V.139, T.140, N.153, Y.170, L.172, D.325 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:Y.170 NAG-NAG.11: 8 residues within 4Å: Chain H: N.26, G.27, Y.28, R.62, Y.87 Chain K: E.280, N.281 Ligands: NAG.41 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:Y.28 Hydrogen bonds: H:R.62, H:R.62 NAG-NAG.13: 5 residues within 4Å: Chain K: N.390, S.392 Ligands: NAG-NAG-NAG.14, NAG-NAG-NAG.14, NAG.39 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 6 residues within 4Å: Chain Q: V.139, T.140, N.153, Y.170, L.172, D.325 1 PLIP interactions: 1 interactions with chain Q Hydrophobic interactions: Q:Y.170 NAG-NAG.18: 8 residues within 4Å: Chain N: N.26, G.27, Y.28, R.62, Y.87 Chain Q: E.280, N.281 Ligands: NAG.51 3 PLIP interactions: 3 interactions with chain N Hydrophobic interactions: N:Y.28 Hydrogen bonds: N:R.62, N:R.62 NAG-NAG.20: 5 residues within 4Å: Chain Q: N.390, S.392 Ligands: NAG-NAG-NAG.21, NAG-NAG-NAG.21, NAG.49 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.2: 14 residues within 4Å: Chain C: Y.33, G.55, D.56, T.57, N.58, F.114, T.115 Chain D: W.86, D.87, S.88, R.90, T.92 Chain E: N.142, I.143 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.58, C:T.115, C:N.58 NAG-NAG-BMA-MAN-MAN.9: 14 residues within 4Å: Chain I: Y.33, G.55, D.56, T.57, N.58, F.114, T.115 Chain J: W.86, D.87, S.88, R.90, T.92 Chain K: N.142, I.143 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:N.58, I:T.115, I:T.57, I:N.58 NAG-NAG-BMA-MAN-MAN.16: 14 residues within 4Å: Chain O: Y.33, G.55, D.56, T.57, N.58, F.114, T.115 Chain P: W.86, D.87, S.88, R.90, T.92 Chain Q: N.142, I.143 2 PLIP interactions: 2 interactions with chain O Hydrogen bonds: O:N.58, O:T.115, O:T.57, O:N.58

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.3: 10 residues within 4Å: Chain E: S.214, E.216, P.217, V.259, L.266, N.267, N.381, V.449, S.450 Ligands: NAG.30 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:V.449 Hydrogen bonds: E:S.214 NAG-NAG-BMA-MAN.10: 10 residues within 4Å: Chain K: S.214, E.216, P.217, V.259, L.266, N.267, N.381, V.449, S.450 Ligands: NAG.40 1 PLIP interactions: 1 interactions with chain K Hydrophobic interactions: K:V.449 Hydrogen bonds: K:S.214 NAG-NAG-BMA-MAN.17: 10 residues within 4Å: Chain Q: S.214, E.216, P.217, V.259, L.266, N.267, N.381, V.449, S.450 Ligands: NAG.50 1 PLIP interactions: 1 interactions with chain Q Hydrophobic interactions: Q:V.449 Hydrogen bonds: Q:S.214

3 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.5: 19 residues within 4Å: Chain C: R.103, I.104, G.106, V.107, V.108 Chain D: S.22, N.42, N.43, N.44, P.58, G.59, S.60 Chain E: N.300, C.301, T.302, R.331, H.334, N.336, T.418 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain C Hydrogen bonds: E:R.331, E:R.331, C:R.103 Hydrophobic interactions: C:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN.12: 19 residues within 4Å: Chain I: R.103, I.104, G.106, V.107, V.108 Chain J: S.22, N.42, N.43, N.44, P.58, G.59, S.60 Chain K: N.300, C.301, T.302, R.331, H.334, N.336, T.418 3 PLIP interactions: 2 interactions with chain K, 1 interactions with chain I Hydrogen bonds: K:R.331, K:R.331, I:R.103 Hydrophobic interactions: I:V.108 NAG-NAG-BMA-MAN-MAN-MAN-MAN.19: 19 residues within 4Å: Chain O: R.103, I.104, G.106, V.107, V.108 Chain P: S.22, N.42, N.43, N.44, P.58, G.59, S.60 Chain Q: N.300, C.301, T.302, R.331, H.334, N.336, T.418 3 PLIP interactions: 2 interactions with chain Q, 1 interactions with chain O Hydrogen bonds: Q:R.331, Q:R.331, O:R.103 Hydrophobic interactions: O:V.108

3 x NAG- NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG.7: 7 residues within 4Å: Chain E: N.367, S.368, T.376, N.390, S.392 Ligands: NAG-NAG.6, NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.14: 7 residues within 4Å: Chain K: N.367, S.368, T.376, N.390, S.392 Ligands: NAG-NAG.13, NAG-NAG.13 No protein-ligand interaction detected (PLIP) NAG-NAG-NAG.21: 7 residues within 4Å: Chain Q: N.367, S.368, T.376, N.390, S.392 Ligands: NAG-NAG.20, NAG-NAG.20 No protein-ligand interaction detected (PLIP)

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

NAG.22: 3 residues within 4Å: Chain E: E.92, N.93 Chain F: S.17 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain E: N.138, K.152 Ligand excluded by PLIP NAG.24: 6 residues within 4Å: Chain E: T.133, Q.135, S.155, F.156, N.157, K.168 Ligand excluded by PLIP NAG.25: 7 residues within 4Å: Chain A: H.73, A.74, S.75, W.76 Chain E: R.197, N.202, T.203 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain E: Q.298, N.300, S.338 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain E: N.306, T.308, I.327, V.445 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain E: N.343, S.397, W.399 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain E: G.393, N.396 Ligands: NAG-NAG.6 Ligand excluded by PLIP NAG.30: 6 residues within 4Å: Chain E: N.267, L.270, P.296, V.449, N.451 Ligands: NAG-NAG-BMA-MAN.3 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain E: K.237, N.239 Ligands: NAG-NAG.4 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain K: E.92, N.93 Chain L: S.17 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain K: N.138, K.152 Ligand excluded by PLIP NAG.34: 6 residues within 4Å: Chain K: T.133, Q.135, S.155, F.156, N.157, K.168 Ligand excluded by PLIP NAG.35: 7 residues within 4Å: Chain G: H.73, A.74, S.75, W.76 Chain K: R.197, N.202, T.203 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain K: Q.298, N.300, S.338 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain K: N.306, T.308, I.327, V.445 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain K: N.343, S.397, W.399 Ligand excluded by PLIP NAG.39: 3 residues within 4Å: Chain K: G.393, N.396 Ligands: NAG-NAG.13 Ligand excluded by PLIP NAG.40: 6 residues within 4Å: Chain K: N.267, L.270, P.296, V.449, N.451 Ligands: NAG-NAG-BMA-MAN.10 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain K: K.237, N.239 Ligands: NAG-NAG.11 Ligand excluded by PLIP NAG.42: 3 residues within 4Å: Chain Q: E.92, N.93 Chain R: S.17 Ligand excluded by PLIP NAG.43: 2 residues within 4Å: Chain Q: N.138, K.152 Ligand excluded by PLIP NAG.44: 6 residues within 4Å: Chain Q: T.133, Q.135, S.155, F.156, N.157, K.168 Ligand excluded by PLIP NAG.45: 7 residues within 4Å: Chain M: H.73, A.74, S.75, W.76 Chain Q: R.197, N.202, T.203 Ligand excluded by PLIP NAG.46: 3 residues within 4Å: Chain Q: Q.298, N.300, S.338 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain Q: N.306, T.308, I.327, V.445 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain Q: N.343, S.397, W.399 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain Q: G.393, N.396 Ligands: NAG-NAG.20 Ligand excluded by PLIP NAG.50: 6 residues within 4Å: Chain Q: N.267, L.270, P.296, V.449, N.451 Ligands: NAG-NAG-BMA-MAN.17 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain Q: K.237, N.239 Ligands: NAG-NAG.18 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

3BNC117 Fab heavy chain: AGM
3BNC117 Fab light chain: BHN
PGT122 Fab heavy chain: CIO
PGT122 Fab light chain: DJP
HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp120: EKQ
Envelope glycoprotein gp160: FLR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

G
K

M
P

B
L

H
N

N
R

C
G

I
J

O
O

D
I

J
M

P
Q

E
A

K
C

Q
E

F
B

L
D

R
F

3BNC117 Fab heavy chain

3BNC117 Fab light chain

PGT122 Fab heavy chain

PGT122 Fab light chain

HIV-1 Envelope Glycoprotein BG505 SOSIP.664 gp120

Envelope glycoprotein gp160

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