MolNFT v1 · #86462 · protein
Structure of a liganded bacterial catalase
4B7F: “Structure of a liganded bacterial catalase”. X-ray diffraction, 4 ligands (NDP, HEM, NO), 20 pockets (best druggability 0.86). MolNFT v1 #86462 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4B7F
- Type
- protein
- Length
- 2,057 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalase
- EC
- 1.11.1.6
- UniProt
- A0A0U4WRC5
- Ligands
- NDP, HEM, NO, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Catalase (EC 1.11.1.6) | protein | 515 | 30% helix, 18% strand | A0A0U4WRC5 |
| B, C, D | Catalase (EC 1.11.1.6) | protein | 514 | 31% helix, 18% strand | A0A0U4WRC5 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, C, B, D
- NO · Nitric oxide · ion · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 2 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, C, D
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 555 | 0.86 | 0.92 | 46 | CL |
| 2 | 229 | 0.84 | 0.97 | 39 | NO, HEM |
| 3 | 227 | 0.84 | 0.97 | 36 | NO, HEM |
| 4 | 236 | 0.84 | 0.96 | 37 | NO, HEM |
| 5 | 233 | 0.83 | 0.96 | 38 | NO, HEM |
Interfaces
6 interfaces between chains.
- A–B · 5367 Ų buried · 79 hydrogen bonds · protein-protein
- C–D · 5357 Ų buried · 81 hydrogen bonds · protein-protein
- B–D · 4258 Ų buried · 66 hydrogen bonds · protein-protein
- A–C · 4183 Ų buried · 65 hydrogen bonds · protein-protein
- B–C · 3215 Ų buried · 65 hydrogen bonds · protein-protein
Compared structures
- 4B7F · Structure of a liganded bacterial catalase · 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 A0A0U4WRC5
- Elsewhere: RCSB PDB 4B7F · PDBe 4B7F · UniProt A0A0U4WRC5
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