Research workbench
Crystal structure of human prostate specific antigen complexed with an activating antibody
Analyse Crystal structure of human prostate specific antigen complexed with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZCL
- Type
- protein
- Length
- 685 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prostate-specific antigen; Monoclonal antibody 8G8F5 Fab
- EC
- 3.4.21.77
- UniProt
- P07288
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | Prostate-specific antigen (EC 3.4.21.77) | protein | 237 | 12% helix, 33% strand | P07288 |
| L | Monoclonal antibody 8G8F5 Fab | protein | 218 | 5% helix, 54% strand | — |
| H | Monoclonal antibody 8G8F5 Fab | protein | 230 | 7% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 364 | 0.63 | 0.79 | 47 | empty |
| 2 | 464 | 0.59 | 0.75 | 57 | empty |
| 3 | 62 | 0.57 | 0.89 | 20 | empty |
| 4 | 157 | 0.55 | 0.81 | 30 | empty |
| 5 | 103 | 0.48 | 0.81 | 19 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1940 Ų buried · 19 hydrogen bonds · protein-protein
- P–H · 691 Ų buried · 10 hydrogen bonds · protein-protein
- P–L · 224 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 2ZCL · Crystal structure of human prostate specific antigen complexed with an activating antibody · 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 2ZCL · PDBe 2ZCL · UniProt P07288
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