Research workbench
Crystal structure of ketosteroid isomerase D40N from pseudomonas putida (pksi) with bound phenol
Analyse Crystal structure of ketosteroid isomerase D40N from pseudomonas putida (pksi)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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