SMTL ID : 9hvi.1

PSMA in complex with nanobody 8

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 2.46 Å

Oligo State

hetero-2-2-mer

Ligands

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Non-covalent)

NAG-NAG.1: 4 residues within 4Å: Chain A: N.21, Q.40, S.43, Q.44 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 4 residues within 4Å: Chain B: N.21, Q.40, S.43, Q.44 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.40, B:Q.44

2 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.3: 4 residues within 4Å: Chain A: S.417, N.421, P.539, Q.596 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.596, A:Q.596, A:Q.596 NAG-NAG-BMA.5: 5 residues within 4Å: Chain B: S.417, L.418, N.421, P.539, Q.596 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.596

2 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: 8 residues within 4Å: Chain A: S.576, S.579, A.580, N.583, Q.685 Chain B: E.221, Y.222, R.299 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.221, B:R.299 NAG-NAG-BMA-MAN-MAN.6: 7 residues within 4Å: Chain A: E.221, Y.222, R.299 Chain B: S.576, S.579, N.583, Q.685 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.299, A:R.299

8 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-covalent)

NAG.7: 2 residues within 4Å: Chain A: N.66, T.294 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:T.294 Hydrogen bonds: A:N.66 NAG.8: 5 residues within 4Å: Chain A: Y.72, E.82, I.83, N.85 Chain C: G.57 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.72, A:E.82, A:E.82 NAG.9: 1 residues within 4Å: Chain A: N.140 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.140 NAG.10: 5 residues within 4Å: Chain A: W.191, G.403, N.404, F.510, Y.511 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.510 NAG.14: 2 residues within 4Å: Chain B: N.66, T.294 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:T.294 Hydrogen bonds: B:N.66 NAG.15: 6 residues within 4Å: Chain B: Y.72, E.82, I.83, N.85 Chain D: G.57, I.59 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Y.72, B:E.82, B:E.82 Hydrophobic interactions: D:I.59 NAG.16: 1 residues within 4Å: Chain B: N.140 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:N.140 NAG.17: 4 residues within 4Å: Chain B: W.191, N.404, F.510, Y.511 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:F.510

4 x ZN: ZINC ION(Non-covalent)

ZN.11: 5 residues within 4Å: Chain A: D.332, E.370, Y.497, H.498 Ligands: ZN.12 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.332, A:E.370, A:H.498 ZN.12: 5 residues within 4Å: Chain A: H.322, D.332, E.369, D.398 Ligands: ZN.11 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.322, A:D.332, A:D.398, A:D.398 ZN.18: 5 residues within 4Å: Chain B: D.332, E.370, Y.497, H.498 Ligands: ZN.19 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.332, B:E.370, B:E.370, B:H.498 ZN.19: 6 residues within 4Å: Chain B: H.322, D.332, P.333, E.369, D.398 Ligands: ZN.18 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.322, B:D.332, B:D.398, B:D.398

2 x CA: CALCIUM ION(Non-covalent)

CA.13: 5 residues within 4Å: Chain A: D.211, T.214, Y.217, E.378, E.381 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:T.214, A:T.214, A:E.378, A:E.378, A:E.381 CA.20: 5 residues within 4Å: Chain B: D.211, T.214, Y.217, E.378, E.381 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:T.214, B:T.214, B:Y.217, B:E.378, B:E.381

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.21: 3 residues within 4Å: Chain B: D.398, R.479, R.525 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Alon-Zchut, G. et al., Structural analysis of nanobody interactions with their prostate-specific membrane antigen binding epitopes. Int.J.Biol.Macromol. (2025)

Release Date

2025-07-16

Peptides

Glutamate carboxypeptidase 2: AB
Nano body 8: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

C
H

D
Q

Glutamate carboxypeptidase 2

Nano body 8

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