MolNFT v1 · #79621 · protein
Crystal structure of ketosteroid isomerase Y16AD103A from pseudomonas putida
3T8N · Steroid delta-isomerase: “Crystal structure of ketosteroid isomerase Y16AD103A from pseudomonas putida”. X-ray diffraction, 2 ligands (EDT, SO4), 6 pockets (best druggability 0.74). MolNFT v1 #79621 on GenesisL1: 3D structure…
- PDB
- 3T8N
- Type
- protein
- Length
- 516 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
- EDT, SO4
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Steroid delta-isomerase (EC 5.3.3.1) | protein | 129 | 30% helix, 40% strand | P07445 |
| B | Steroid delta-isomerase (EC 5.3.3.1) | protein | 130 | 29% helix, 39% strand | P07445 |
| D | Steroid delta-isomerase (EC 5.3.3.1) | protein | 127 | 30% helix, 38% strand | P07445 |
| F | Steroid delta-isomerase (EC 5.3.3.1) | protein | 130 | 28% helix, 39% strand | P07445 |
Ligands and binding sites
- EDT · {[-(bis-carboxymethyl-amino)-ethyl]-carboxymethyl-amino}-acetic acid · ligand · chains D, F
- SO4 · Sulfate ion · ion · 5 copies · chains A, 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 | 215 | 0.74 | 0.88 | 28 | empty |
| 2 | 248 | 0.72 | 0.86 | 32 | empty |
| 3 | 195 | 0.72 | 0.87 | 29 | empty |
| 4 | 228 | 0.69 | 0.85 | 32 | empty |
| 5 | 70 | 0.33 | 0.75 | 16 | SO4 |
Interfaces
2 interfaces between chains.
- A–B · 1088 Ų buried · 20 hydrogen bonds · protein-protein
- D–F · 1078 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3T8N · Crystal structure of ketosteroid isomerase Y16AD103A from Pseudomonas putida · 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 3T8N · PDBe 3T8N · UniProt P07445
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