SMTL ID : 9hvk.1

PSMA in complex with nanobody 7 and 8

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.00 Å

Oligo State

hetero-2-2-2-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: 5 residues within 4Å: Chain A: N.21, Q.40, S.43, Q.44, E.47 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.44 NAG-NAG.2: 4 residues within 4Å: Chain B: N.21, Q.40, S.43, Q.44 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: 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: 3 residues within 4Å: Chain A: N.421, Q.596, D.597 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.5: 4 residues within 4Å: Chain B: S.417, N.421, Q.596, D.597 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.596, B:D.597

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.579, N.583, Q.685 Chain B: H.57, D.59, E.221, Y.222, R.299 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.57 NAG-NAG-BMA-MAN-MAN.6: 9 residues within 4Å: Chain A: H.57, E.221, Y.222, R.299 Chain B: S.576, S.579, A.580, N.583, Q.685 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.221, A:R.299, A:R.299, A:H.57

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

NAG.7: 2 residues within 4Å: Chain A: N.66, H.69 No protein-ligand interaction detected (PLIP) NAG.8: 6 residues within 4Å: Chain A: E.82, I.83, F.84, N.85 Chain F: G.56, I.69 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain F Hydrogen bonds: A:E.82, A:E.82, A:N.85, F:G.56 NAG.9: 2 residues within 4Å: Chain A: N.140, S.142 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.142 NAG.10: 6 residues within 4Å: Chain A: W.191, G.403, N.404, E.431, F.510, Y.511 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.191 Hydrogen bonds: A:W.191, A:N.404, A:N.404, A:E.431, A:F.510 NAG.14: 3 residues within 4Å: Chain B: N.66, T.68, H.69 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.68, B:H.69 NAG.15: 5 residues within 4Å: Chain B: E.82, I.83, N.85 Chain E: G.56, I.69 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:N.85 Hydrogen bonds: B:E.82, B:E.82, B:N.85 NAG.16: 2 residues within 4Å: Chain B: N.140, S.142 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.142 NAG.17: 6 residues within 4Å: Chain B: W.191, G.403, N.404, E.431, F.510, Y.511 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.191 Hydrogen bonds: B:W.191, B:N.404, B:E.431, B:F.510

4 x ZN: ZINC ION(Non-covalent)

ZN.11: 6 residues within 4Å: Chain A: R.155, R.200, G.201, W.326, E.370, H.498 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:R.200, A:H.498 ZN.12: 5 residues within 4Å: Chain A: H.322, D.332, E.369, E.370, D.398 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.322, A:D.332, A:D.398 ZN.18: 5 residues within 4Å: Chain B: R.155, Q.199, R.200, G.201, H.498 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:R.200, B:H.498 ZN.19: 4 residues within 4Å: Chain B: H.322, E.369, E.370, D.398 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.322, 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:Y.217, 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:E.378, B:E.378, B:E.381

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

CL.21: 6 residues within 4Å: Chain B: N.396, A.397, D.398, N.464, R.479, R.481 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
Nanobody 7: CD
Nanobody 8: EF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
E

C
H

D
Q

E
P

F
M

Glutamate carboxypeptidase 2

Nanobody 7

Nanobody 8

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