MolNFT v1 · #125767 · protein
Crystal structure of myxobacterial CYP260A1
5LIV · Cytochrome P450 CYP260A1,CYTOCHROME P450 CYP260A1: “Crystal structure of myxobacterial CYP260A1”. X-ray diffraction, 2 ligands (HEM, SO4), 18 pockets (best druggability 0.87). MolNFT v1 #125767 on GenesisL1: 3D structure, binding…
- PDB
- 5LIV
- Type
- protein
- Length
- 1,570 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome P450 CYP260A1,CYTOCHROME P450 CYP260A1
- EC
- 1.14.-.-
- UniProt
- A9FDB7
- Ligands
- HEM, SO4
- Pockets
- 18 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome P450 CYP260A1,CYTOCHROME P450 CYP260A1 (EC 1.14.-.-) | protein | 397 | 54% helix, 10% strand | A9FDB7 |
| B | Cytochrome P450 CYP260A1,CYTOCHROME P450 CYP260A1 (EC 1.14.-.-) | protein | 389 | 53% helix, 11% strand | A9FDB7 |
| C | Cytochrome P450 CYP260A1,CYTOCHROME P450 CYP260A1 (EC 1.14.-.-) | protein | 395 | 54% helix, 10% strand | A9FDB7 |
| D | Cytochrome P450 CYP260A1,CYTOCHROME P450 CYP260A1 (EC 1.14.-.-) | protein | 389 | 55% helix, 10% strand | A9FDB7 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 17 copies · chains A, D, B, C
- GOL · Glycerol · additive · 11 copies · chains A, D, B, C
- DMS · Dimethyl sulfoxide · additive · 6 copies · chains A, B, C, D
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 660 | 0.87 | 0.92 | 55 | HEM, GOL |
| 2 | 635 | 0.87 | 0.92 | 55 | HEM, GOL |
| 3 | 630 | 0.86 | 0.90 | 53 | HEM, GOL |
| 4 | 857 | 0.84 | 0.86 | 76 | HEM |
| 5 | 439 | 0.80 | 0.88 | 66 | SO4, GOL |
Interfaces
3 interfaces between chains.
- B–C · 1103 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 998 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 187 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5LIV · Crystal structure of myxobacterial CYP260A1 · 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 A9FDB7
- Elsewhere: RCSB PDB 5LIV · PDBe 5LIV · UniProt A9FDB7
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