Research workbench
Cryo-EM structure of W107R after heme uptake (1HEME molecule) katg from M. tuberculosis
Analyse Cryo-EM structure of W107R after heme uptake (1HEME molecule) katg from M.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7A7C
- Type
- protein
- Length
- 1,226 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalase-peroxidase
- EC
- 1.11.1.21
- UniProt
- A0A0D5ZBI4
- Ligands
- HEM
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 45% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Catalase-peroxidase (EC 1.11.1.21) | protein | 560 | 49% helix, 3% strand | A0A0D5ZBI4 |
| B | Catalase-peroxidase (EC 1.11.1.21) | protein | 666 | 43% helix, 6% strand | A0A0D5ZBI4 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.83 | 0.89 | 65 | HEM |
| 2 | 237 | 0.76 | 0.90 | 34 | empty |
| 3 | 414 | 0.73 | 0.84 | 59 | empty |
| 4 | 73 | 0.67 | 0.94 | 18 | empty |
| 5 | 569 | 0.65 | 0.76 | 50 | empty |
Interfaces
1 interface between chains.
- A–B · 2490 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 7A7C · Cryo-EM structure of W107R after heme uptake (1heme molecule) KatG from M. tuberculosis · 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 A0A0D5ZBI4
- Elsewhere: RCSB PDB 7A7C · PDBe 7A7C · UniProt A0A0D5ZBI4
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