Research workbench
Crystal structure of delta 5-3-ketosteroid isomerase from mycobacterium sp.
Analyse Crystal structure of delta 5-3-ketosteroid isomerase from mycobacterium sp. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Z3R
- Type
- protein
- Length
- 1,047 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Steroid delta-isomerase
- UniProt
- V5XH97
- Pockets
- 14 · best druggability 0.88
Structure
x-ray diffraction · 5 distinct chains · 26% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H, E, B | Steroid delta-isomerase | protein | 131 | 26% helix, 44% strand | V5XH97 |
| D | Steroid delta-isomerase | protein | 129 | 27% helix, 43% strand | V5XH97 |
| F | Steroid delta-isomerase | protein | 133 | 25% helix, 44% strand | V5XH97 |
| C | Steroid delta-isomerase | protein | 130 | 25% helix, 44% strand | V5XH97 |
| G | Steroid delta-isomerase | protein | 131 | 24% helix, 44% strand | V5XH97 |
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1058 | 0.88 | 0.90 | 129 | empty |
| 2 | 553 | 0.77 | 0.83 | 63 | empty |
| 3 | 192 | 0.73 | 0.89 | 30 | empty |
| 4 | 217 | 0.73 | 0.88 | 33 | empty |
| 5 | 195 | 0.72 | 0.88 | 30 | empty |
Interfaces
11 interfaces between chains.
- C–E · 918 Ų buried · 18 hydrogen bonds · protein-protein
- D–H · 906 Ų buried · 16 hydrogen bonds · protein-protein
- A–G · 892 Ų buried · 16 hydrogen bonds · protein-protein
- F–B · 883 Ų buried · 13 hydrogen bonds · protein-protein
- A–F · 687 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5Z3R · Crystal Structure of Delta 5-3-Ketosteroid Isomerase from Mycobacterium sp. · 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 V5XH97
- Elsewhere: RCSB PDB 5Z3R · PDBe 5Z3R · UniProt V5XH97
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