MolNFT v1 · #115530 · protein
Crystal structure of the esterase domain from rhodothermus marinus RMAR_1206 protein
5CML · Osmc family protein: “Crystal structure of the esterase domain from rhodothermus marinus RMAR_1206 protein”. X-ray diffraction, 4 pockets (best druggability 0.52). MolNFT v1 #115530 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5CML
- Type
- protein
- Length
- 466 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Osmc family protein
- UniProt
- D0MHY8
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Osmc family protein | protein | 240 | 38% helix, 26% strand | D0MHY8 |
| B | Osmc family protein | protein | 226 | 38% helix, 25% strand | D0MHY8 |
Ligands and binding sites
- PGE · Triethylene glycol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 192 | 0.52 | 0.77 | 23 | empty |
| 2 | 112 | 0.46 | 0.78 | 16 | PGE |
| 3 | 77 | 0.35 | 0.76 | 18 | empty |
| 4 | 64 | 0.31 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 953 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5CML · Crystal structure of the Esterase domain from Rhodothermus marinus Rmar_1206 protein · 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 D0MHY8
- Elsewhere: RCSB PDB 5CML · PDBe 5CML · UniProt D0MHY8
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