MolNFT v1 · #121658 · protein
Crystal structure of crmk, a flavoenzyme involved in the shunt product recycling mechanism in caerulomycin biosynthesis
5I1W: “Crystal structure of crmk, a flavoenzyme involved in the shunt product recycling mechanism in caerulomycin…”. X-ray diffraction, 3 ligands (FAD, 67L, 67K), 12 pockets (best druggability 0.90). MolNFT v1 #121658 on GenesisL1: 3D…
- PDB
- 5I1W
- Type
- protein
- Length
- 1,992 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Crmk
- UniProt
- H8Y6P5
- Ligands
- FAD, 67L, 67K
- Pockets
- 12 · best druggability 0.90
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Crmk | protein | 498 | 33% helix, 23% strand | H8Y6P5 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- 67L · 6-(hydroxymethyl)[2,2'-bipyridin]-4-ol · ligand · 3 copies · chains A, B, C
- 67K · 4-hydroxy[2,2'-bipyridine]-6-carbaldehyde · ligand · chains 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1047 | 0.90 | 0.92 | 119 | FAD, 67L |
| 2 | 467 | 0.88 | 0.96 | 76 | FAD, 67K |
| 3 | 460 | 0.86 | 0.93 | 62 | FAD, 67L |
| 4 | 286 | 0.84 | 0.95 | 58 | FAD, 67L |
| 5 | 162 | 0.79 | 0.95 | 32 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1814 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1808 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 610 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 cofactor (flavinylation).
Compared structures
- 5I1W · 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 5I1W · PDBe 5I1W · UniProt H8Y6P5
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