SMTL ID : 8flw.1

Cryo-EM Structure of PGT145 DU303 Fab in complex with BG505 DS-SOSIP.664

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-1-3-3-mer

Ligands

14 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: 3 residues within 4Å: Chain E: R.162, I.164, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain E: Q.263, N.265, S.303 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 5 residues within 4Å: Chain E: N.332, S.333, T.341 Ligands: NAG-NAG.5, NAG-NAG.5 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 5 residues within 4Å: Chain E: N.355, S.357 Ligands: NAG-NAG.4, NAG-NAG.4, NAG.36 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain G: R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain G: Q.263, N.265, V.414 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 6 residues within 4Å: Chain G: N.332, S.333, T.341 Ligands: NAG-NAG.13, NAG-NAG.13, NAG.48 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 5 residues within 4Å: Chain G: N.355, S.357 Ligands: NAG-NAG.12, NAG-NAG.12, NAG.48 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 4 residues within 4Å: Chain H: V.144, R.162, I.164, N.167 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:V.144, H:I.164 NAG-NAG.17: 3 residues within 4Å: Chain H: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain H: Q.263, N.265, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.19: 7 residues within 4Å: Chain H: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG.20, NAG-NAG.20 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 5 residues within 4Å: Chain H: N.355, S.357 Ligands: NAG-NAG.19, NAG-NAG.19, NAG.57 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 4 residues within 4Å: Chain H: N.106, N.118, Y.135, D.290 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:Y.135 Hydrogen bonds: H:Y.135

4 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.2: 14 residues within 4Å: Chain E: K.35, S.179, E.181, V.224, L.231, N.232, N.346, C.347, I.407, Q.408, C.413, V.414, S.415 Ligands: NAG.37 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.6: 7 residues within 4Å: Chain A: N.31, H.53, E.54, K.101, H.102, R.103 Chain E: N.122 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.103, A:R.103 NAG-NAG-BMA-MAN-MAN-MAN.9: 10 residues within 4Å: Chain G: K.35, E.181, N.232, N.346, G.348, I.407, Q.408, V.414, S.415 Ligands: NAG.49 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN-MAN.16: 11 residues within 4Å: Chain H: S.179, E.181, L.231, N.232, R.274, N.346, G.348, I.407, V.414, S.415 Ligands: NAG-NAG-BMA.21 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:G.348

5 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.7: 3 residues within 4Å: Chain E: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.10: 3 residues within 4Å: Chain G: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.14: 8 residues within 4Å: Chain A: D.56, K.57 Chain G: Q.100, S.120, F.121, N.122, K.131, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.21: 4 residues within 4Å: Chain H: P.261, V.414, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.16 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.22: 11 residues within 4Å: Chain A: Y.107, E.119 Chain B: Q.30, H.31, S.32, T.33 Chain H: Q.100, S.120, F.121, N.122, K.131 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.31

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

NAG.24: 2 residues within 4Å: Chain C: N.100, S.102 Ligand excluded by PLIP NAG.25: 1 residues within 4Å: Chain C: N.126 Ligand excluded by PLIP NAG.26: 2 residues within 4Å: Chain D: N.100, S.102 Ligand excluded by PLIP NAG.27: 1 residues within 4Å: Chain D: N.126 Ligand excluded by PLIP NAG.28: 3 residues within 4Å: Chain C: S.17 Chain E: E.57, N.58 Ligand excluded by PLIP NAG.29: 3 residues within 4Å: Chain E: N.103, G.114, K.117 Ligand excluded by PLIP NAG.30: 3 residues within 4Å: Chain E: N.106, N.118, D.290 Ligand excluded by PLIP NAG.31: 3 residues within 4Å: Chain E: N.204, T.206, S.244 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain E: N.271, T.273, I.292 Ligand excluded by PLIP NAG.33: 4 residues within 4Å: Chain E: H.299, N.301, S.381, T.383 Ligand excluded by PLIP NAG.34: 1 residues within 4Å: Chain E: N.308 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain E: N.324 Ligand excluded by PLIP NAG.36: 3 residues within 4Å: Chain E: N.361 Ligands: NAG-NAG.5, NAG-NAG.5 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain E: P.261, V.414, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.2 Ligand excluded by PLIP NAG.38: 2 residues within 4Å: Chain F: N.100, S.102 Ligand excluded by PLIP NAG.39: 1 residues within 4Å: Chain F: N.126 Ligand excluded by PLIP NAG.40: 4 residues within 4Å: Chain D: G.16, S.17 Chain G: E.57, N.58 Ligand excluded by PLIP NAG.41: 2 residues within 4Å: Chain G: N.103, K.159 Ligand excluded by PLIP NAG.42: 5 residues within 4Å: Chain G: V.104, N.118, S.120, L.137, D.290 Ligand excluded by PLIP NAG.43: 4 residues within 4Å: Chain G: N.204, T.206, S.244, E.245 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain G: N.271 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain G: H.299, N.301, S.381 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain G: N.308 Ligand excluded by PLIP NAG.47: 1 residues within 4Å: Chain G: N.324 Ligand excluded by PLIP NAG.48: 3 residues within 4Å: Chain G: N.361 Ligands: NAG-NAG.12, NAG-NAG.13 Ligand excluded by PLIP NAG.49: 4 residues within 4Å: Chain G: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.9 Ligand excluded by PLIP NAG.50: 2 residues within 4Å: Chain F: T.18 Chain H: N.58 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain H: N.103 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain H: N.204, S.244 Ligand excluded by PLIP NAG.53: 1 residues within 4Å: Chain H: N.271 Ligand excluded by PLIP NAG.54: 5 residues within 4Å: Chain H: T.267, H.299, N.301, S.381, T.383 Ligand excluded by PLIP NAG.55: 2 residues within 4Å: Chain H: K.304, N.308 Ligand excluded by PLIP NAG.56: 1 residues within 4Å: Chain H: N.324 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain H: N.361 Ligands: NAG-NAG.20 Ligand excluded by PLIP NAG.58: 4 residues within 4Å: Chain H: N.106, N.107, G.293, D.294 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Holt, G.T. et al., Improved HIV-1 neutralization breadth and potency of V2-apex antibodies by in silico design. Cell Rep (2023)

Release Date

2023-05-31

Peptides

PGT145 DU303 Heavy: A
PGT145 DU303 Light: B
Envelope glycoprotein gp41: CDF
Envelope glycoprotein gp120: EGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
A

D
B

F
F

E
C

G
G

H
I

PGT145 DU303 Heavy

PGT145 DU303 Light

Envelope glycoprotein gp41

Envelope glycoprotein gp120

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