SMTL ID : 9ehm.1

Structure of HIV-1 BG505 SOSIP.664 Env trimer in complex with IOMAmin5 and 10-1074 Broadly Neutralizing Antibodies - Class II

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-2-2-3-3-mer

Ligands

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.1: 6 residues within 4Å: Chain A: V.129, T.130, N.143, Y.160, L.162 Chain N: R.91 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.160 Hydrogen bonds: A:Y.160 NAG-NAG.2: 5 residues within 4Å: Chain A: Q.125, S.145, F.146, N.147, K.158 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.125 NAG-NAG.3: 5 residues within 4Å: Chain A: V.169, R.187, I.189, N.192, T.193 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:I.189 NAG-NAG.5: 5 residues within 4Å: Chain A: N.296, I.317, V.435 Chain N: N.63, F.64 1 PLIP interactions: 1 interactions with chain N Hydrogen bonds: N:N.63 NAG-NAG.6: 4 residues within 4Å: Chain A: N.380, S.382, R.412 Ligands: NAG.34 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain B: V.129, N.143, Y.160, L.162, D.315 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.160 Hydrogen bonds: B:Y.160, B:Y.160 NAG-NAG.9: 5 residues within 4Å: Chain B: T.123, Q.125, F.146, N.147 Chain C: D.154 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain B: E.270, N.271, T.273 Chain G: W.107 Chain I: G.31, F.32 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain B: N.296, I.317, G.434, V.435 Chain O: F.64 1 PLIP interactions: 1 interactions with chain O Hydrophobic interactions: O:F.64 NAG-NAG.15: 4 residues within 4Å: Chain B: N.380, P.410 Ligands: NAG-NAG.16, NAG-NAG.16 No protein-ligand interaction detected (PLIP) NAG-NAG.16: 7 residues within 4Å: Chain B: N.357, S.358, T.366, N.380, S.382 Ligands: NAG-NAG.15, NAG-NAG.15 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 5 residues within 4Å: Chain C: Q.125, S.145, F.146, N.147, K.158 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 5 residues within 4Å: Chain C: N.296, I.317, V.435 Chain P: F.64, G.65 1 PLIP interactions: 1 interactions with chain P Hydrogen bonds: P:G.65 NAG-NAG.23: 6 residues within 4Å: Chain C: N.357, S.358, T.366, S.382 Ligands: NAG-NAG.24, NAG-NAG.24 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 9 residues within 4Å: Chain C: N.380, S.382, G.383, T.408, L.409, P.410 Ligands: NAG-NAG.23, NAG-NAG.23, NAG.47 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- MAN- BMA: beta-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-BMA.4: 15 residues within 4Å: Chain A: E.206, P.207, V.249, L.256, N.257, N.371, C.372, G.373, V.435, I.436, R.437, C.438, V.439, S.440 Ligands: NAG.33 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.439 Hydrogen bonds: A:C.372, A:V.439, A:V.439, A:E.206, A:V.435, A:R.437 NAG-NAG-MAN-BMA.11: 14 residues within 4Å: Chain B: K.60, E.206, P.207, L.256, N.257, F.370, N.371, C.372, G.373, R.437, C.438, V.439, S.440 Ligands: NAG.40 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.439 Hydrogen bonds: B:V.439, B:K.60, B:E.206, B:E.206

2 x NAG- NAG- BMA- BMA: beta-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-BMA.7: 13 residues within 4Å: Chain A: N.290, C.291, T.292, R.321, H.324, N.326 Chain K: R.103, I.104, Y.105, G.106 Chain N: S.24, D.61, I.62 6 PLIP interactions: 2 interactions with chain A, 2 interactions with chain N, 2 interactions with chain K Hydrogen bonds: A:R.321, A:R.321, N:S.24, N:D.61, K:R.103, K:R.103 NAG-NAG-BMA-BMA.20: 13 residues within 4Å: Chain C: E.206, P.207, V.249, L.256, N.257, N.371, C.372, G.373, R.437, C.438, V.439, S.440 Ligands: NAG.48 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.439 Hydrogen bonds: C:E.206, C:R.437, C:V.439

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.10: 11 residues within 4Å: Chain B: R.187, N.192, T.193 Chain C: R.303 Chain G: T.19, V.20, S.21, T.71, S.75, I.76, Y.80 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:Y.80, G:T.19, G:T.71, G:T.19, G:V.20 NAG-NAG-BMA-MAN.14: 15 residues within 4Å: Chain B: T.292, R.321, H.324, N.326, S.406, T.408 Chain L: R.103, I.104, Y.105, G.106, V.107 Chain O: S.24, D.61, I.62, N.63 10 PLIP interactions: 2 interactions with chain B, 6 interactions with chain O, 2 interactions with chain L Hydrogen bonds: B:R.321, B:R.321, O:S.24, O:S.24, O:D.61, O:D.61, O:N.63, O:N.63, L:R.103, L:R.103 NAG-NAG-BMA-MAN.19: 9 residues within 4Å: Chain A: R.303 Chain C: V.169, R.187, N.192, T.193 Chain H: T.19, D.73, S.75, Y.80 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.17: 4 residues within 4Å: Chain C: V.129, N.143, Y.160, L.162 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.160 NAG-NAG-MAN.21: 6 residues within 4Å: Chain C: N.271, T.273 Chain H: W.107 Chain J: R.27, G.31, F.32 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:R.27, J:R.27, J:R.27

1 x NAG- NAG- BMA- MAN- BMA- BMA: beta-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-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-BMA-BMA.25: 18 residues within 4Å: Chain C: N.290, D.319, R.321, H.324, N.326, S.406, T.408 Chain M: R.103, I.104, Y.105, G.106, V.107 Chain P: S.24, N.44, N.45, Q.46, D.61, N.63 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain P Hydrogen bonds: C:D.319, P:S.24, P:N.63

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

NAG.26: 3 residues within 4Å: Chain A: K.329, N.333, S.387 Ligand excluded by PLIP NAG.27: 5 residues within 4Å: Chain A: E.82, N.83 Chain D: G.16, S.17, T.18 Ligand excluded by PLIP NAG.28: 4 residues within 4Å: Chain A: N.128, K.142, R.165, Y.186 Ligand excluded by PLIP NAG.29: 8 residues within 4Å: Chain A: N.229, T.231, G.232, I.267, R.268, S.269, I.272, H.346 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain A: N.271, T.273, N.274, K.277 Ligand excluded by PLIP NAG.31: 4 residues within 4Å: Chain A: Q.288, N.290, S.328, S.406 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain A: G.383, N.386, I.407 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain A: L.260, P.286, N.441 Ligands: NAG-NAG-MAN-BMA.4 Ligand excluded by PLIP NAG.34: 6 residues within 4Å: Chain A: N.357, S.358, S.359, G.360, T.366 Ligands: NAG-NAG.6 Ligand excluded by PLIP NAG.35: 4 residues within 4Å: Chain B: K.329, N.333, S.387, W.389 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain B: E.82, N.83 Chain E: S.17 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain B: N.229, G.230, T.231, S.269 Ligand excluded by PLIP NAG.38: 6 residues within 4Å: Chain B: Q.288, N.290, N.326, S.328, R.437, V.439 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain B: N.386 Ligand excluded by PLIP NAG.40: 3 residues within 4Å: Chain B: P.286, N.441 Ligands: NAG-NAG-MAN-BMA.11 Ligand excluded by PLIP NAG.41: 7 residues within 4Å: Chain B: N.128, T.130, G.139, K.142, R.165, K.184, Y.186 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain C: K.329, N.333 Ligand excluded by PLIP NAG.43: 5 residues within 4Å: Chain C: E.82, N.83 Chain F: G.13, G.16, S.17 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain C: N.128, K.142, R.165, Y.186 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain C: N.229, G.230, T.231 Ligand excluded by PLIP NAG.46: 5 residues within 4Å: Chain C: Q.288, N.290, S.328, R.437, V.439 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain C: G.383, N.386 Ligands: NAG-NAG.24 Ligand excluded by PLIP NAG.48: 6 residues within 4Å: Chain C: N.257, L.260, P.286, V.439, N.441 Ligands: NAG-NAG-BMA-BMA.20 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain D: N.100, S.101, S.102, Y.127 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain D: K.122, E.123, S.125, N.126 Ligand excluded by PLIP NAG.51: 4 residues within 4Å: Chain E: N.100, S.102, W.103, L.134 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain E: K.122, E.123, N.126, Y.127 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain F: N.100, S.101, S.102 Ligand excluded by PLIP NAG.54: 4 residues within 4Å: Chain F: K.122, E.123, S.125, N.126 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Dam, K.A. et al., Mapping essential somatic hypermutations in a CD4-binding site bNAb informs HIV-1 vaccine design. Cell Rep (2025)

Release Date

2025-05-21

Peptides

HIV-1 BG505 SOSIP gp120,Envelope glycoprotein gp120: ABC
HIV-1 BG505 SOSIP gp41: DEF
IOMAmin5 Fab Heavy Chain: GH
IOMAmin5 Fab Light Chain: IJ
10-1074 Fab Heavy Chain: KLM
10-1074 Fab Light Chain: NOP

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
H

H
I

I
K

J
L

K
M

L
N

M
O

N
P

O
Q

P
R

HIV-1 BG505 SOSIP gp120,Envelope glycoprotein gp120

HIV-1 BG505 SOSIP gp41

IOMAmin5 Fab Heavy Chain

IOMAmin5 Fab Light Chain

10-1074 Fab Heavy Chain

10-1074 Fab Light Chain

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