SMTL ID : 6x96.1

Cryo-EM model of HIV-1 Env BG505 SOSIP.664 in complex with rabbit monoclonal antibody 10A fragment antigen binding variable domain

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

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.1: 9 residues within 4Å: Chain A: P.217, N.267, F.380, N.381, C.382, G.383, V.449, S.450 Ligands: NAG-NAG.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.449 NAG-NAG-BMA-MAN.5: 9 residues within 4Å: Chain E: P.217, N.267, F.380, N.381, C.382, G.383, V.449, S.450 Ligands: NAG-NAG.6 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:V.449 NAG-NAG-BMA-MAN.9: 9 residues within 4Å: Chain I: P.217, N.267, F.380, N.381, C.382, G.383, V.449, S.450 Ligands: NAG-NAG.10 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:V.449

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.2: 4 residues within 4Å: Chain A: N.267, P.296, N.451 Ligands: NAG-NAG-BMA-MAN.1 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: E.92, N.93 Chain B: S.17 Chain D: S.51 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.51 NAG-NAG.4: 6 residues within 4Å: Chain A: V.139, N.141, N.153, Y.170, L.172, D.325 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.170 Hydrogen bonds: A:Y.170 NAG-NAG.6: 4 residues within 4Å: Chain E: N.267, P.296, N.451 Ligands: NAG-NAG-BMA-MAN.5 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 4 residues within 4Å: Chain E: E.92, N.93 Chain F: S.17 Chain H: S.51 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:S.51 NAG-NAG.8: 6 residues within 4Å: Chain E: V.139, N.141, N.153, Y.170, L.172, D.325 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:Y.170 Hydrogen bonds: E:Y.170 NAG-NAG.10: 4 residues within 4Å: Chain I: N.267, P.296, N.451 Ligands: NAG-NAG-BMA-MAN.9 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 4 residues within 4Å: Chain I: E.92, N.93 Chain J: S.17 Chain L: S.51 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:S.51 NAG-NAG.12: 6 residues within 4Å: Chain I: V.139, N.141, N.153, Y.170, L.172, D.325 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:Y.170 Hydrogen bonds: I:Y.170

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

NAG.13: 3 residues within 4Å: Chain A: N.390, S.392 Ligands: NAG.14 Ligand excluded by PLIP NAG.14: 4 residues within 4Å: Chain A: N.367, S.368, G.370 Ligands: NAG.13 Ligand excluded by PLIP NAG.15: 3 residues within 4Å: Chain A: N.306, I.327, V.445 Ligand excluded by PLIP NAG.16: 3 residues within 4Å: Chain A: Q.298, N.300, S.338 Ligand excluded by PLIP NAG.17: 6 residues within 4Å: Chain A: N.300, T.302, H.334, N.336, T.418, R.447 Ligand excluded by PLIP NAG.18: 2 residues within 4Å: Chain A: S.392, N.396 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: N.343, E.344, W.399 Ligand excluded by PLIP NAG.20: 1 residues within 4Å: Chain A: N.138 Ligand excluded by PLIP NAG.21: 4 residues within 4Å: Chain A: Q.135, S.155, F.156, N.157 Ligand excluded by PLIP NAG.22: 6 residues within 4Å: Chain A: V.179, R.197, L.198, I.199, C.201, N.202 Ligand excluded by PLIP NAG.23: 4 residues within 4Å: Chain A: N.239, T.241, S.279, I.282 Ligand excluded by PLIP NAG.24: 3 residues within 4Å: Chain E: N.390, S.392 Ligands: NAG.25 Ligand excluded by PLIP NAG.25: 4 residues within 4Å: Chain E: N.367, S.368, G.370 Ligands: NAG.24 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain E: N.306, I.327, V.445 Ligand excluded by PLIP NAG.27: 3 residues within 4Å: Chain E: Q.298, N.300, S.338 Ligand excluded by PLIP NAG.28: 6 residues within 4Å: Chain E: N.300, T.302, H.334, N.336, T.418, R.447 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain E: S.392, N.396 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain E: N.343, E.344, W.399 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain E: N.138 Ligand excluded by PLIP NAG.32: 4 residues within 4Å: Chain E: Q.135, S.155, F.156, N.157 Ligand excluded by PLIP NAG.33: 6 residues within 4Å: Chain E: V.179, R.197, L.198, I.199, C.201, N.202 Ligand excluded by PLIP NAG.34: 4 residues within 4Å: Chain E: N.239, T.241, S.279, I.282 Ligand excluded by PLIP NAG.35: 3 residues within 4Å: Chain I: N.390, S.392 Ligands: NAG.36 Ligand excluded by PLIP NAG.36: 4 residues within 4Å: Chain I: N.367, S.368, G.370 Ligands: NAG.35 Ligand excluded by PLIP NAG.37: 3 residues within 4Å: Chain I: N.306, I.327, V.445 Ligand excluded by PLIP NAG.38: 3 residues within 4Å: Chain I: Q.298, N.300, S.338 Ligand excluded by PLIP NAG.39: 6 residues within 4Å: Chain I: N.300, T.302, H.334, N.336, T.418, R.447 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain I: S.392, N.396 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain I: N.343, E.344, W.399 Ligand excluded by PLIP NAG.42: 1 residues within 4Å: Chain I: N.138 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain I: Q.135, S.155, F.156, N.157 Ligand excluded by PLIP NAG.44: 6 residues within 4Å: Chain I: V.179, R.197, L.198, I.199, C.201, N.202 Ligand excluded by PLIP NAG.45: 4 residues within 4Å: Chain I: N.239, T.241, S.279, I.282 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ozorowski, G. et al., Limited breadth of anti-HIV Env glycan hole antibodies is further hindered by strain-specific peptide interactions. To Be Published

Release Date

2021-12-08

Peptides

BG505 HIV-1 Env gp120: AEI
BG505 HIV-1 Env gp41: BFJ
monoclonal antibody 10A fragment antigen binding heavy chain: CGK
monoclonal antibody 10A kappa chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
C

I
G

B
B

F
D

J
I

C
H

G
E

K
J

D
L

H
F

L
K

BG505 HIV-1 Env gp120

BG505 HIV-1 Env gp41

monoclonal antibody 10A fragment antigen binding heavy chain

monoclonal antibody 10A kappa chain

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