Research workbench
MET8P: a bifunctional NAD-dependent dehydrogenase and ferrochelatase involved in siroheme synthesis.
Analyse MET8P: a bifunctional NAD-dependent dehydrogenase and ferrochelatase involved… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KYQ
- Type
- protein
- Length
- 797 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Siroheme biosynthesis protein MET8
- EC
- 1.-.-.-, 4.99.1.1
- UniProt
- P15807
- Ligands
- NAD
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Siroheme biosynthesis protein MET8 (EC 1.-.-.-, 4.99.1.1) | protein | 262 | 47% helix, 21% strand | P15807 |
| B | Siroheme biosynthesis protein MET8 (EC 1.-.-.-, 4.99.1.1) | protein | 273 | 43% helix, 18% strand | P15807 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1018 | 0.72 | 0.76 | 90 | empty |
| 2 | 392 | 0.63 | 0.78 | 36 | empty |
| 3 | 485 | 0.60 | 0.75 | 63 | empty |
| 4 | 302 | 0.54 | 0.75 | 30 | empty |
| 5 | 82 | 0.45 | 0.81 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3525 Ų buried · 61 hydrogen bonds · protein-protein
- A–C · 592 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 29 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 modified (engineered).
Compared structures
- 1KYQ · Met8p: A bifunctional NAD-dependent dehydrogenase and ferrochelatase involved in siroheme… · the same entry in another collection · chain A against A, TM-score 1.00
- P15807 · AlphaFold monomer V2.0 prediction for siroheme biosynthesis protein MET8 (P15807) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P15807
- Elsewhere: RCSB PDB 1KYQ · PDBe 1KYQ · UniProt P15807
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