MolNFT v1 · #121657 · protein
Crystal structure of crmk, a flavoenzyme involved in the shunt product recycling mechanism in caerulomycin biosynthesis
5I1V: “Crystal structure of crmk, a flavoenzyme involved in the shunt product recycling mechanism in caerulomycin…”. X-ray diffraction, 1 ligand (FAD), 15 pockets (best druggability 0.89). MolNFT v1 #121657 on GenesisL1: 3D structure…
- PDB
- 5I1V
- Type
- protein
- Length
- 1,991 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Crmk
- UniProt
- H8Y6P5
- Ligands
- FAD
- Pockets
- 15 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Crmk | protein | 498 | 32% helix, 22% strand | H8Y6P5 |
| C | Crmk | protein | 497 | 32% helix, 23% strand | H8Y6P5 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 621 | 0.89 | 0.94 | 89 | FAD |
| 2 | 365 | 0.86 | 0.95 | 53 | FAD |
| 3 | 356 | 0.85 | 0.94 | 52 | FAD |
| 4 | 346 | 0.85 | 0.94 | 61 | FAD |
| 5 | 216 | 0.80 | 0.94 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1837 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 1810 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 532 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (flavinylation).
Compared structures
- 5I1V · Crystal structure of CrmK, a flavoenzyme involved in the shunt product recycling… · 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 H8Y6P5
- Elsewhere: RCSB PDB 5I1V · PDBe 5I1V · UniProt H8Y6P5
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