Research workbench
X-ray structure of human prostate-specific membrane antigen(PSMA) in complex with a inhibitor Glu-490
Analyse X-ray structure of human prostate-specific membrane antigen(PSMA) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BFZ
- Type
- protein
- Length
- 694 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.73
- Source
- Homo sapiens
- Molecule
- Glutamate carboxypeptidase 2
- EC
- 3.4.17.21
- UniProt
- Q04609
- Ligands
- TKZ, NAG, BMA, MAN, FUC, ZN, NA, CA, CL
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · resolution 1.73 · 1 distinct chain · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamate carboxypeptidase 2 (EC 3.4.17.21) | protein | 694 | 38% helix, 19% strand | Q04609 |
Ligands and binding sites
- TKZ · (((S)-1-carboxy-5-((E)-2-cyano-3-(5-(1-(3-methoxy-3-oxopropyl)-1,2,3,4-tetrahydroquinolin-6-yl)thiophen-2-yl)acrylamido)pentyl)carbamoyl)-L-glutamic acid · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 12 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 4 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 2 copies
- FUC · alpha-L-fucopyranose · sugar · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- CA · Calcium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 728 | 0.79 | 0.83 | 79 | EDO, TKZ |
| 2 | 367 | 0.59 | 0.76 | 51 | empty |
| 3 | 151 | 0.52 | 0.80 | 37 | empty |
| 4 | 74 | 0.38 | 0.78 | 16 | empty |
| 5 | 71 | 0.30 | 0.74 | 21 | empty |
Modifications
Observed in the structure: 7 glycan (N-glycosylation).
Compared structures
- 7BFZ · X-ray structure of human prostate-specific membrane ANTIGEN(PSMA) in complex with a… · the same entry in another collection · chain A against A, TM-score 1.00
- Q04609 · AlphaFold monomer V2.0 prediction for glutamate carboxypeptidase 2 (Q04609) · a predicted model of the same protein · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q04609
- Elsewhere: RCSB PDB 7BFZ · PDBe 7BFZ · UniProt Q04609
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