Research workbench
Structure of the heme domain of cooa from rhodospirillum rubrum
Analyse Structure of the heme domain of cooa from rhodospirillum rubrum in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4K8F
- Type
- protein
- Length
- 528 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcriptional regulator, CRP/FNR family
- UniProt
- Q2RUG3
- Ligands
- HEM
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Transcriptional regulator, CRP/FNR family | protein | 132 | 30% helix, 29% strand | Q2RUG3 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, B, C, D
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 | 178 | 0.68 | 0.86 | 27 | HEM |
| 2 | 141 | 0.67 | 0.87 | 23 | HEM |
| 3 | 145 | 0.65 | 0.86 | 28 | HEM |
| 4 | 145 | 0.65 | 0.86 | 22 | HEM |
| 5 | 66 | 0.36 | 0.78 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1351 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 1325 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 28 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4K8F · Structure of the heme domain of CooA from Rhodospirillum rubrum · 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 Q2RUG3
- Elsewhere: RCSB PDB 4K8F · PDBe 4K8F · UniProt Q2RUG3
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