Research workbench
Crystal structure of a racemase from streptomyces coelicolor A3(2) with bound magnesium
Analyse Crystal structure of a racemase from streptomyces coelicolor A3(2) with bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CK5
- Type
- protein
- Length
- 1,405 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative racemase
- UniProt
- Q9RKF7
- Ligands
- MG
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Putative racemase | protein | 357 | 41% helix, 24% strand | Q9RKF7 |
| D | Putative racemase | protein | 334 | 41% helix, 20% strand | Q9RKF7 |
Ligands and binding sites
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 205 | 0.82 | 0.96 | 53 | empty |
| 2 | 167 | 0.80 | 0.96 | 40 | empty |
| 3 | 563 | 0.78 | 0.84 | 64 | empty |
| 4 | 527 | 0.74 | 0.82 | 56 | empty |
| 5 | 412 | 0.72 | 0.82 | 48 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1891 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1881 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 219 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 41 modified (engineered).
Compared structures
- 3CK5 · Crystal structure of a racemase from Streptomyces coelicolor A3(2) with bound magnesium · 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 Q9RKF7
- Elsewhere: RCSB PDB 3CK5 · PDBe 3CK5 · UniProt Q9RKF7
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