SMTL ID : 8fis.1

Structure of Bispecific CAP256V2LS-J3 Fab in complex with BG505 DS-SOSIP.664

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-3-3-3-1-mer

Ligands

8 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: 3 residues within 4Å: Chain C: R.162, N.167 Chain J: G.63 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.12: 3 residues within 4Å: Chain C: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.16: 4 residues within 4Å: Chain E: V.104, N.118, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.17: 5 residues within 4Å: Chain C: R.278 Chain E: V.144, R.162, N.167 Chain H: G.63 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.27: 6 residues within 4Å: Chain E: N.332, S.333, T.341, S.357 Ligands: NAG-NAG.23, NAG-NAG.23 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.29: 3 residues within 4Å: Chain E: N.246, T.248, N.249 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.30: 4 residues within 4Å: Chain E: R.278 Chain F: R.162, N.167 Chain G: G.63 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.40: 6 residues within 4Å: Chain F: N.332, T.341, N.355, S.357 Ligands: NAG-NAG.36, NAG-NAG.36 No protein-ligand interaction detected (PLIP)

22 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: 3 residues within 4Å: Chain C: N.204, T.206, S.244 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 8 residues within 4Å: Chain C: Q.263, N.265, N.301, V.302, S.303, R.412, V.414 Ligands: NAG-NAG.6 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 8 residues within 4Å: Chain C: N.265, T.267, H.299, N.301, S.381, T.383, R.412 Ligands: NAG-NAG.4 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 6 residues within 4Å: Chain C: N.355, S.357 Ligands: NAG-NAG.8, NAG-NAG-BMA-MAN-MAN.10, NAG-NAG-BMA-MAN-MAN.10, NAG-NAG-BMA-MAN-MAN.10 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 5 residues within 4Å: Chain C: S.357, G.358, N.361 Ligands: NAG-NAG.7, NAG-NAG.7 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 2 residues within 4Å: Chain C: N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain C: N.103, Y.161 Ligands: NAG-NAG-BMA-MAN-MAN.10 No protein-ligand interaction detected (PLIP) NAG-NAG.13: 4 residues within 4Å: Chain A: G.16, S.17 Chain C: E.57, N.58 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 4 residues within 4Å: Chain E: N.204, T.206, S.244, H.321 No protein-ligand interaction detected (PLIP) NAG-NAG.20: 6 residues within 4Å: Chain E: Q.263, N.265, N.301, V.302, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.22: 5 residues within 4Å: Chain E: T.267, H.299, N.301, T.383, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.23: 6 residues within 4Å: Chain E: N.355, S.357 Ligands: NAG-NAG.24, NAG-NAG-BMA.27, NAG-NAG-BMA.27, NAG-NAG-BMA.27 No protein-ligand interaction detected (PLIP) NAG-NAG.24: 3 residues within 4Å: Chain E: N.361 Ligands: NAG-NAG.23, NAG-NAG.23 No protein-ligand interaction detected (PLIP) NAG-NAG.25: 4 residues within 4Å: Chain E: L.235, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.19 No protein-ligand interaction detected (PLIP) NAG-NAG.26: 2 residues within 4Å: Chain E: N.122, K.133 No protein-ligand interaction detected (PLIP) NAG-NAG.28: 2 residues within 4Å: Chain E: N.103, K.117 No protein-ligand interaction detected (PLIP) NAG-NAG.31: 3 residues within 4Å: Chain F: N.204, T.206, S.244 No protein-ligand interaction detected (PLIP) NAG-NAG.33: 6 residues within 4Å: Chain F: Q.263, N.265, N.301, V.302, S.303, R.412 No protein-ligand interaction detected (PLIP) NAG-NAG.35: 6 residues within 4Å: Chain F: N.265, T.267, H.299, N.301, S.381, T.383 No protein-ligand interaction detected (PLIP) NAG-NAG.36: 5 residues within 4Å: Chain F: N.355, S.357 Ligands: NAG-NAG-BMA.40, NAG-NAG-BMA.40, NAG-NAG-BMA.40 No protein-ligand interaction detected (PLIP) NAG-NAG.37: 1 residues within 4Å: Chain F: N.361 No protein-ligand interaction detected (PLIP) NAG-NAG.38: 5 residues within 4Å: Chain F: L.235, P.261, V.414, N.416 Ligands: NAG-NAG-BMA-MAN.32 No protein-ligand interaction detected (PLIP)

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.3: 11 residues within 4Å: Chain C: E.181, K.222, L.231, N.232, N.346, G.348, R.412, C.413, V.414, S.415 Ligands: NAG-NAG-BMA-MAN-MAN.15 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.19: 10 residues within 4Å: Chain E: E.181, L.231, N.232, N.346, C.347, G.348, C.413, V.414, S.415 Ligands: NAG-NAG.25 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:G.348 NAG-NAG-BMA-MAN.32: 9 residues within 4Å: Chain F: E.181, P.182, N.232, N.346, G.348, C.413, V.414, S.415 Ligands: NAG-NAG.38 No protein-ligand interaction detected (PLIP)

3 x NAG- NAG- BMA- MAN: 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.5: 4 residues within 4Å: Chain C: N.271, I.292, V.410 Chain H: F.17 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.21: 3 residues within 4Å: Chain E: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN.34: 3 residues within 4Å: Chain F: N.271, I.292, V.410 No protein-ligand interaction detected (PLIP)

5 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.10: 8 residues within 4Å: Chain C: N.332, S.333, T.341, N.355, S.357 Ligands: NAG-NAG.7, NAG-NAG.7, NAG-NAG.11 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.14: 6 residues within 4Å: Chain C: V.104, N.106, N.118, S.120, Y.135, D.290 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.15: 5 residues within 4Å: Chain C: N.232, L.235, P.261, N.416 Ligands: NAG-NAG-BMA-MAN.3 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA-MAN-MAN.39: 7 residues within 4Å: Chain F: T.98, Q.100, S.120, N.122, K.131 Chain I: W.108, Q.118 1 PLIP interactions: 1 interactions with chain I Hydrogen bonds: I:Q.118 NAG-NAG-BMA-MAN-MAN.41: 5 residues within 4Å: Chain F: N.106, N.118, Y.135, D.290 Chain J: K.190 No protein-ligand interaction detected (PLIP)

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

NAG.42: 2 residues within 4Å: Chain A: N.100, S.102 Ligand excluded by PLIP NAG.43: 1 residues within 4Å: Chain A: N.126 Ligand excluded by PLIP NAG.44: 1 residues within 4Å: Chain A: N.107 Ligand excluded by PLIP NAG.45: 2 residues within 4Å: Chain B: N.100, S.102 Ligand excluded by PLIP NAG.46: 1 residues within 4Å: Chain B: N.126 Ligand excluded by PLIP NAG.47: 3 residues within 4Å: Chain B: N.107, S.109, E.110 Ligand excluded by PLIP NAG.48: 2 residues within 4Å: Chain C: K.304, N.308 Ligand excluded by PLIP NAG.49: 1 residues within 4Å: Chain C: N.324 Ligand excluded by PLIP NAG.50: 4 residues within 4Å: Chain C: N.106, N.107, I.291, G.293 Ligand excluded by PLIP NAG.51: 1 residues within 4Å: Chain C: N.430 Ligand excluded by PLIP NAG.52: 2 residues within 4Å: Chain D: N.100, S.102 Ligand excluded by PLIP NAG.53: 2 residues within 4Å: Chain D: N.126, Y.127 Ligand excluded by PLIP NAG.54: 1 residues within 4Å: Chain D: N.107 Ligand excluded by PLIP NAG.55: 1 residues within 4Å: Chain E: N.58 Ligand excluded by PLIP NAG.56: 2 residues within 4Å: Chain E: N.308, W.364 Ligand excluded by PLIP NAG.57: 2 residues within 4Å: Chain E: K.316, N.324 Ligand excluded by PLIP NAG.58: 3 residues within 4Å: Chain E: N.106, N.107, G.293 Ligand excluded by PLIP NAG.59: 1 residues within 4Å: Chain E: N.430 Ligand excluded by PLIP NAG.60: 3 residues within 4Å: Chain B: S.17 Chain F: E.57, N.58 Ligand excluded by PLIP NAG.61: 1 residues within 4Å: Chain F: N.103 Ligand excluded by PLIP NAG.62: 3 residues within 4Å: Chain F: N.246, T.248, N.249 Ligand excluded by PLIP NAG.63: 2 residues within 4Å: Chain F: K.304, N.308 Ligand excluded by PLIP NAG.64: 1 residues within 4Å: Chain F: N.324 Ligand excluded by PLIP NAG.65: 3 residues within 4Å: Chain F: N.106, N.107, D.294 Ligand excluded by PLIP NAG.66: 2 residues within 4Å: Chain F: T.429, N.430 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, B. et al., Bispecific antibody CAP256.J3LS targets V2-apex and CD4-binding sites with high breadth and potency. Mabs (2023)

Release Date

2023-02-01

Peptides

Envelope glycoprotein gp41: ABD
Envelope glycoprotein gp120: CEF
J3-VRC26.25 Light: GHJ
VRC26.25 Heavy: I

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
E

C
C

E
F

F
G

G
J

H
I

J
L

I
H

Envelope glycoprotein gp41

Envelope glycoprotein gp120

J3-VRC26.25 Light

VRC26.25 Heavy

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