Research workbench
Structure of the FAD and heme binding protein MSMEG_4975 from mycobacterium smegmatis
Analyse Structure of the FAD and heme binding protein MSMEG_4975 from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YBN
- Type
- protein
- Length
- 419 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Flavin-nucleotide-binding protein
- UniProt
- A0R238
- Ligands
- HEM, FAD, NI, SO4
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 23% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Flavin-nucleotide-binding protein | protein | 214 | 24% helix, 36% strand | A0R238 |
| B | Flavin-nucleotide-binding protein | protein | 205 | 22% helix, 40% strand | A0R238 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B
- NI · Nickel (II) ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 735 | 0.80 | 0.84 | 66 | HEM, FAD |
| 2 | 295 | 0.78 | 0.89 | 41 | empty |
| 3 | 475 | 0.71 | 0.81 | 52 | HEM, FAD |
| 4 | 99 | 0.49 | 0.82 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 3195 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 4YBN · Structure of the FAD and Heme binding protein msmeg_4975 from Mycobacterium smegmatis · 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 A0R238
- Elsewhere: RCSB PDB 4YBN · PDBe 4YBN · UniProt A0R238
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