MolNFT v1 · #48649 · protein
Crystal structure of ketosteroid isomerase D40N from pseudomonas putida (pksi) with bound phenol
2PZV · Steroid delta-isomerase: “Crystal structure of ketosteroid isomerase D40N from pseudomonas putida (pksi) with bound phenol”. X-ray diffraction, 1 ligand (IPH), 6 pockets (best druggability 0.75). MolNFT v1 #48649 on GenesisL1: 3D…
- PDB
- 2PZV
- Type
- protein
- Length
- 492 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Steroid delta-isomerase
- EC
- 5.3.3.1
- UniProt
- P07445
- Ligands
- IPH
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Steroid delta-isomerase (EC 5.3.3.1) | protein | 123 | 31% helix, 41% strand | P07445 |
Ligands and binding sites
- IPH · Phenol · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 212 | 0.75 | 0.90 | 33 | IPH |
| 2 | 212 | 0.74 | 0.89 | 34 | IPH |
| 3 | 194 | 0.60 | 0.81 | 24 | IPH |
| 4 | 192 | 0.60 | 0.81 | 25 | IPH |
| 5 | 59 | 0.28 | 0.74 | 16 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1099 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1087 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 791 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 107 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 41 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2PZV · Crystal Structure of Ketosteroid Isomerase D40N from Pseudomonas Putida (pksi) with bound… · the same entry in another collection · 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 P07445
- Elsewhere: RCSB PDB 2PZV · PDBe 2PZV · UniProt P07445
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