SMTL ID : 8fk5.1

Cryo-EM Structure of PG9RSH DU011 Fab in complex with BG505 DS-SOSIP.664

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-1-1-mer

Ligands

16 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: 4 residues within 4Å: Chain C: S.120, F.121, N.122, K.131 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain C: R.162, N.167 Chain E: R.278 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 3 residues within 4Å: Chain C: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 4 residues within 4Å: Chain C: Q.263, N.265, R.412, V.414 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain C: N.332, T.341, N.355, S.357 Ligands: NAG-NAG.7, NAG-NAG.7 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 5 residues within 4Å: Chain C: N.355, S.357 Ligands: NAG-NAG.6, NAG-NAG.6, NAG.37 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain E: R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 5 residues within 4Å: Chain E: Q.263, N.265, S.303, R.412, V.414 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 7 residues within 4Å: Chain E: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG.12, NAG-NAG.12 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 5 residues within 4Å: Chain E: N.355, S.357 Ligands: NAG-NAG.11, NAG-NAG.11, NAG.50 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 3 residues within 4Å: Chain E: P.261, Q.263, N.416 No protein-ligand interaction detected (PLIP) NAG-NAG.15: 3 residues within 4Å: Chain C: R.278 Chain F: R.162, N.167 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 2 residues within 4Å: Chain F: N.246, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 3 residues within 4Å: Chain F: Q.263, N.265, V.414 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 5 residues within 4Å: Chain F: N.355, S.357 Ligands: NAG-NAG-BMA-MAN-MAN.19, NAG-NAG-BMA-MAN-MAN.19, NAG.60 No protein-ligand interaction detected (PLIP) NAG-NAG.21: 3 residues within 4Å: Chain F: P.261, Q.263, N.416 No protein-ligand interaction detected (PLIP)

3 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.3: 11 residues within 4Å: Chain C: S.179, E.181, P.182, N.232, N.346, G.348, Q.408, C.413, V.414, S.415 Ligands: NAG.38 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:G.348 NAG-NAG-BMA-MAN-MAN-MAN.9: 9 residues within 4Å: Chain E: S.179, E.181, N.232, N.346, G.348, R.412, C.413, V.414, S.415 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:V.414 NAG-NAG-BMA-MAN-MAN-MAN.16: 8 residues within 4Å: Chain F: E.181, P.182, L.231, N.232, G.348, Q.408, C.413, V.414 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:V.414 Hydrogen bonds: F:G.348, F:V.414

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.14: 7 residues within 4Å: Chain E: T.98, Q.100, S.120, N.122 Chain G: Y.120, Y.122 Chain H: S.58 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:S.58, H:S.58 NAG-NAG-BMA-MAN-MAN.19: 5 residues within 4Å: Chain F: N.332, T.341, S.357 Ligands: NAG-NAG.20, NAG-NAG.20 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.22: 10 residues within 4Å: Chain F: V.104, N.106, N.118, Y.135, L.137, D.290 Chain G: D.53, S.55, F.113, Y.114 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:F.113, G:Y.114 Hydrogen bonds: G:Y.114, G:Y.114

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-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-MAN-MAN-MAN-MAN-MAN.23: 17 residues within 4Å: Chain F: T.98, Q.100, S.120, N.122 Chain G: D.103, R.105, Y.110, Y.118, N.119, Y.120, H.121 Chain H: E.33, S.34, D.52, V.53, K.55, L.93 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain G Hydrogen bonds: F:Q.100, G:D.103 Hydrophobic interactions: G:Y.118

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

NAG.24: 2 residues within 4Å: Chain A: N.100, S.102 Ligand excluded by PLIP NAG.25: 3 residues within 4Å: Chain A: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.26: 1 residues within 4Å: Chain A: N.107 Ligand excluded by PLIP NAG.27: 2 residues within 4Å: Chain B: N.100, S.102 Ligand excluded by PLIP NAG.28: 1 residues within 4Å: Chain B: N.126 Ligand excluded by PLIP NAG.29: 2 residues within 4Å: Chain C: E.57, N.58 Ligand excluded by PLIP NAG.30: 2 residues within 4Å: Chain C: N.103, R.113 Ligand excluded by PLIP NAG.31: 5 residues within 4Å: Chain C: V.104, N.106, N.118, Y.135, D.290 Ligand excluded by PLIP NAG.32: 3 residues within 4Å: Chain C: N.204, T.206, S.244 Ligand excluded by PLIP NAG.33: 2 residues within 4Å: Chain C: N.271, I.292 Ligand excluded by PLIP NAG.34: 6 residues within 4Å: Chain C: T.267, H.299, N.301, S.381, T.383, R.412 Ligand excluded by PLIP NAG.35: 1 residues within 4Å: Chain C: N.308 Ligand excluded by PLIP NAG.36: 2 residues within 4Å: Chain C: K.316, N.324 Ligand excluded by PLIP NAG.37: 4 residues within 4Å: Chain C: G.358, N.361 Ligands: NAG-NAG.7, NAG-NAG.7 Ligand excluded by PLIP NAG.38: 4 residues within 4Å: Chain C: N.232, P.261, N.416 Ligands: NAG-NAG-BMA-MAN-MAN-MAN.3 Ligand excluded by PLIP NAG.39: 2 residues within 4Å: Chain C: N.106, N.107 Ligand excluded by PLIP NAG.40: 2 residues within 4Å: Chain D: N.100, S.102 Ligand excluded by PLIP NAG.41: 3 residues within 4Å: Chain D: E.123, N.126, Y.127 Ligand excluded by PLIP NAG.42: 4 residues within 4Å: Chain B: G.16, S.17 Chain E: E.57, N.58 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain E: N.103 Ligand excluded by PLIP NAG.44: 4 residues within 4Å: Chain E: V.104, N.118, Y.135, D.290 Ligand excluded by PLIP NAG.45: 3 residues within 4Å: Chain E: N.204, T.206, S.244 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain E: N.271 Ligand excluded by PLIP NAG.47: 4 residues within 4Å: Chain E: H.299, N.301, T.383, R.412 Ligand excluded by PLIP NAG.48: 1 residues within 4Å: Chain E: N.308 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain E: N.324 Ligand excluded by PLIP NAG.50: 3 residues within 4Å: Chain E: N.361 Ligands: NAG-NAG.12, NAG-NAG.12 Ligand excluded by PLIP NAG.51: 3 residues within 4Å: Chain E: N.106, N.107, G.293 Ligand excluded by PLIP NAG.52: 3 residues within 4Å: Chain E: N.246, T.248, N.249 Ligand excluded by PLIP NAG.53: 3 residues within 4Å: Chain D: S.17 Chain F: E.57, N.58 Ligand excluded by PLIP NAG.54: 2 residues within 4Å: Chain F: N.103, R.113 Ligand excluded by PLIP NAG.55: 4 residues within 4Å: Chain F: N.204, T.206, S.244, E.245 Ligand excluded by PLIP NAG.56: 3 residues within 4Å: Chain F: N.271, I.292, V.410 Ligand excluded by PLIP NAG.57: 3 residues within 4Å: Chain F: T.267, H.299, N.301 Ligand excluded by PLIP NAG.58: 2 residues within 4Å: Chain F: K.304, N.308 Ligand excluded by PLIP NAG.59: 1 residues within 4Å: Chain F: N.324 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain F: N.361 Ligands: NAG-NAG.20, NAG-NAG.20 Ligand excluded by PLIP NAG.61: 2 residues within 4Å: Chain F: N.106, N.107 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

Envelope glycoprotein gp41: ABD
Envelope glycoprotein gp120: CEF
Immunoblobulin G1 Fab heavy chain variable region (Fragment): G
Immunoglobulin lambda-1 light chain-like: H

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
F

C
C

E
G

F
I

G
H

H
L

Envelope glycoprotein gp41

Envelope glycoprotein gp120

Immunoblobulin G1 Fab heavy chain variable region (Fragment)

Immunoglobulin lambda-1 light chain-like

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