MolNFT v1 · #61037 · protein
Crystal structure of ketosteroid isomerase-like protein (YP_049581.1) from erwinia carotovora atroseptica SCRI1043 at 2.40 a resolution
3D9R: “Crystal structure of ketosteroid isomerase-like protein (YP_049581.1) from erwinia carotovora atroseptica…”. X-ray diffraction, 2 ligands (UNL, NA), 2 pockets (best druggability 0.79). MolNFT v1 #61037 on GenesisL1: 3D structure…
- PDB
- 3D9R
- Type
- protein
- Length
- 530 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ketosteroid isomerase-like protein
- UniProt
- Q6D750
- Ligands
- UNL, NA
- Pockets
- 2 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ketosteroid isomerase-like protein | protein | 132 | 28% helix, 50% strand | Q6D750 |
| B, C | Ketosteroid isomerase-like protein | protein | 134 | 28% helix, 51% strand | Q6D750 |
| D | Ketosteroid isomerase-like protein | protein | 130 | 28% helix, 51% strand | Q6D750 |
Ligands and binding sites
- UNL · Unknown ligand · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · chains A
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1011 | 0.79 | 0.80 | 129 | UNL |
| 2 | 209 | 0.68 | 0.85 | 30 | UNL |
Interfaces
5 interfaces between chains.
- A–B · 1088 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1078 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 953 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 127 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 119 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 3D9R · Crystal structure of ketosteroid isomerase-like protein (YP_049581.1) from ERWINIA… · the same entry in another collection · chain B against B, 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 Q6D750
- Elsewhere: RCSB PDB 3D9R · PDBe 3D9R · UniProt Q6D750
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