Research workbench
Crystal structure of a ternary complex between psa, a substrat-acyl intermediate and an activating antibody
Analyse Crystal structure of a ternary complex between psa, a substrat-acyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZCK
- Type
- protein
- Length
- 692 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prostate-specific antigen; Kgissqy; Monoclonal antibody 8G8F5 Fab
- EC
- 3.4.21.77
- UniProt
- P07288
- Ligands
- NAG, MAN
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | Prostate-specific antigen (EC 3.4.21.77) | protein | 237 | 11% helix, 35% strand | P07288 |
| S | Kgissqy | protein | 7 | 0% helix, 43% strand | — |
| L | Monoclonal antibody 8G8F5 Fab | protein | 218 | 5% helix, 49% strand | — |
| H | Monoclonal antibody 8G8F5 Fab | protein | 230 | 3% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains P
- MAN · alpha-D-mannopyranose · sugar · chains P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 520 | 0.60 | 0.74 | 59 | empty |
| 2 | 144 | 0.51 | 0.80 | 24 | empty |
| 3 | 124 | 0.49 | 0.80 | 23 | empty |
| 4 | 144 | 0.41 | 0.74 | 24 | empty |
| 5 | 99 | 0.36 | 0.74 | 20 | empty |
Interfaces
4 interfaces between chains.
- L–H · 2032 Ų buried · 30 hydrogen bonds · protein-protein
- P–H · 694 Ų buried · 8 hydrogen bonds · protein-protein
- P–S · 667 Ų buried · 21 hydrogen bonds · protein-protein
- P–L · 237 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 2ZCK · Crystal structure of a ternary complex between PSA, a substrat-acyl intermediate and an… · the same entry in another collection · chain P against P, TM-score 1.00
- P07288 · AlphaFold monomer V2.0 prediction for prostate-specific antigen (P07288) · a predicted model of the same protein · chain P 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 P07288
- Elsewhere: RCSB PDB 2ZCK · PDBe 2ZCK · UniProt P07288
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