SMTL ID : 8to7.1

Cryo-EM structure of HERH-b*01 Fab in complex with HIV-1 Env trimer BG505.DS SOSIP

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-3-mer

Ligands

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.1: 4 residues within 4Å: Chain A: E.57, N.58 Chain B: G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 3 residues within 4Å: Chain B: N.126 Chain H: R.59, D.65 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.6: 3 residues within 4Å: Chain E: N.58 Chain F: G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 4 residues within 4Å: Chain F: E.123, N.126, Y.127 Chain L: D.65 1 PLIP interactions: 1 interactions with chain L Hydrogen bonds: L:D.65 NAG-NAG-BMA.11: 3 residues within 4Å: Chain I: N.58 Chain J: G.16, S.17 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.15: 4 residues within 4Å: Chain D: R.59, D.65 Chain J: N.126, Y.127 No protein-ligand interaction detected (PLIP)

6 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.106, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain A: Q.100, S.120, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 3 residues within 4Å: Chain E: N.106, N.118, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 4 residues within 4Å: Chain E: Q.100, S.120, N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 4 residues within 4Å: Chain I: N.106, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain I: S.120, F.121, N.122, K.133 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.4: 10 residues within 4Å: Chain A: S.179, E.181, V.224, L.231, N.232, C.347, G.348, V.414, S.415 Ligands: NAG.28 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.348 NAG-NAG-BMA-MAN-MAN.9: 11 residues within 4Å: Chain E: S.179, E.181, V.224, L.231, N.232, N.346, C.347, G.348, V.414, S.415 Ligands: NAG.43 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:V.414 Hydrogen bonds: E:G.348 NAG-NAG-BMA-MAN-MAN.14: 11 residues within 4Å: Chain I: S.179, E.181, L.231, N.232, N.346, C.347, G.348, C.413, V.414, S.415 Ligands: NAG.58 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:G.348

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

NAG.16: 4 residues within 4Å: Chain A: N.103, G.114, K.117, R.140 Ligand excluded by PLIP NAG.17: 3 residues within 4Å: Chain A: V.144, R.162, N.167 Ligand excluded by PLIP NAG.18: 4 residues within 4Å: Chain A: N.204, T.206, I.242, H.321 Ligand excluded by PLIP NAG.19: 3 residues within 4Å: Chain A: N.246, T.248, N.249 Ligand excluded by PLIP NAG.20: 5 residues within 4Å: Chain A: Q.263, N.265, V.302, S.303, R.412 Ligand excluded by PLIP NAG.21: 3 residues within 4Å: Chain A: N.271, I.292, V.410 Ligand excluded by PLIP NAG.22: 5 residues within 4Å: Chain A: N.265, T.267, H.299, N.301, R.412 Ligand excluded by PLIP NAG.23: 2 residues within 4Å: Chain A: K.304, N.308 Ligand excluded by PLIP NAG.24: 1 residues within 4Å: Chain A: N.324 Ligand excluded by PLIP NAG.25: 5 residues within 4Å: Chain A: N.332, S.333, S.334, S.357 Ligands: NAG.27 Ligand excluded by PLIP NAG.26: 3 residues within 4Å: Chain A: N.355, S.357 Ligands: NAG.27 Ligand excluded by PLIP NAG.27: 4 residues within 4Å: Chain A: S.357, N.361 Ligands: NAG.25, NAG.26 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain A: P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.4 Ligand excluded by PLIP NAG.29: 1 residues within 4Å: Chain B: N.107 Ligand excluded by PLIP NAG.30: 4 residues within 4Å: Chain B: P.98, W.99, N.100 Chain G: R.31 Ligand excluded by PLIP NAG.31: 1 residues within 4Å: Chain E: N.103 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain E: R.162, N.167 Chain I: R.278 Ligand excluded by PLIP NAG.33: 3 residues within 4Å: Chain E: N.204, I.242, H.321 Ligand excluded by PLIP NAG.34: 3 residues within 4Å: Chain E: N.246, T.248, N.249 Ligand excluded by PLIP NAG.35: 5 residues within 4Å: Chain E: N.265, V.302, S.303, S.381, R.412 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain E: N.271, I.292, V.410 Ligand excluded by PLIP NAG.37: 5 residues within 4Å: Chain E: N.265, T.267, H.299, N.301, R.412 Ligand excluded by PLIP NAG.38: 1 residues within 4Å: Chain E: N.308 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain E: N.324 Ligand excluded by PLIP NAG.40: 5 residues within 4Å: Chain E: N.332, S.333, S.334, S.357 Ligands: NAG.41 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain E: N.355 Ligands: NAG.40, NAG.42 Ligand excluded by PLIP NAG.42: 2 residues within 4Å: Chain E: N.361 Ligands: NAG.41 Ligand excluded by PLIP NAG.43: 3 residues within 4Å: Chain E: P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.9 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain F: N.107 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain F: N.100 Chain K: D.27, R.31 Ligand excluded by PLIP NAG.46: 4 residues within 4Å: Chain I: N.103, G.114, K.117, R.140 Ligand excluded by PLIP NAG.47: 2 residues within 4Å: Chain I: R.162, N.167 Ligand excluded by PLIP NAG.48: 4 residues within 4Å: Chain I: N.204, T.206, I.242, H.321 Ligand excluded by PLIP NAG.49: 3 residues within 4Å: Chain I: N.246, T.248, N.249 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain I: N.265, S.303, R.412 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain I: N.271, I.292, V.410 Ligand excluded by PLIP NAG.52: 4 residues within 4Å: Chain I: N.265, T.267, H.299, N.301 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain I: K.304, N.308, S.362 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain I: N.324 Ligand excluded by PLIP NAG.55: 5 residues within 4Å: Chain I: N.332, S.333, S.334, S.357 Ligands: NAG.56 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain I: N.355, S.357 Ligands: NAG.55 Ligand excluded by PLIP NAG.57: 1 residues within 4Å: Chain I: N.361 Ligand excluded by PLIP NAG.58: 4 residues within 4Å: Chain I: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN.14 Ligand excluded by PLIP NAG.59: 1 residues within 4Å: Chain J: N.107 Ligand excluded by PLIP NAG.60: 5 residues within 4Å: Chain C: R.31, Y.34 Chain J: P.98, W.99, N.100 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, H. et al., Broad and potent HIV-1 neutralization in fusion peptide-primed SHIV-boosted macaques. To Be Published

Release Date

2024-08-07

Peptides

Surface protein gp120: AEI
Transmembrane protein gp41: BFJ
HERH-b*01 heavy chain: CGK
HERH-b*01 light chain: DHL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
E

E
D

I
F

B
B

F
A

J
C

C
H

G
G

K
I

D
L

H
J

L
K

Surface protein gp120

Transmembrane protein gp41

HERH-b*01 heavy chain

HERH-b*01 light chain

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