Research workbench
Crystal structure of mhud R26S mutant with two hemes bound per active site
Analyse Crystal structure of mhud R26S mutant with two hemes bound per active site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6DS7
- Type
- protein
- Length
- 198 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heme-degrading monooxygenase hmob
- EC
- 1.14.14.18
- UniProt
- P9WKH3
- Ligands
- HEM, CL
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 24% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Heme-degrading monooxygenase hmob (EC 1.14.14.18) | protein | 99 | 24% helix, 40% strand | P9WKH3 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 435 | 0.64 | 0.77 | 32 | HEM, CL |
| 2 | 446 | 0.64 | 0.77 | 32 | HEM, CL |
| 3 | 78 | 0.32 | 0.74 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1557 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 6DS7 · Crystal structure of MhuD R26S mutant with two hemes bound per active site · the same entry in another collection · chain A against A, TM-score 1.00
- P9WKH3 · AlphaFold monomer V2.0 prediction for heme oxygenase (mycobilin- producing) (P9WKH3) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 P9WKH3
- Elsewhere: RCSB PDB 6DS7 · PDBe 6DS7 · UniProt P9WKH3
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