MolNFT v1 · #86838 · protein
Catalase 3 from neurospora crassa in tetragonal form exposes a modified tetrameric organization
4BIM: “Catalase 3 from neurospora crassa in tetragonal form exposes a modified tetrameric organization”. X-ray diffraction, 1 ligand (HEM), 20 pockets (best druggability 0.87). MolNFT v1 #86838 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4BIM
- Type
- protein
- Length
- 2,721 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalase 3
- EC
- 1.11.1.6
- UniProt
- Q9C169
- Ligands
- HEM
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 30% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Catalase 3 (EC 1.11.1.6) | protein | 681 | 31% helix, 16% strand | Q9C169 |
| B | Catalase 3 (EC 1.11.1.6) | protein | 679 | 31% helix, 16% strand | Q9C169 |
| D | Catalase 3 (EC 1.11.1.6) | protein | 680 | 28% helix, 15% strand | Q9C169 |
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
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 | 1025 | 0.87 | 0.88 | 126 | empty |
| 2 | 249 | 0.85 | 0.97 | 46 | HEM |
| 3 | 251 | 0.85 | 0.97 | 49 | HEM |
| 4 | 767 | 0.85 | 0.88 | 93 | empty |
| 5 | 288 | 0.85 | 0.95 | 50 | HEM |
Interfaces
5 interfaces between chains.
- C–D · 6029 Ų buried · 80 hydrogen bonds · protein-protein
- A–B · 5989 Ų buried · 94 hydrogen bonds · protein-protein
- B–C · 732 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 313 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 301 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4BIM · Catalase 3 from neurospora crassa in tetragonal form exposes a modified tetrameric… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9C169 · AlphaFold monomer V2.0 prediction for catalase-3 (Q9C169) · a predicted model of the same protein · 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 Q9C169
- Elsewhere: RCSB PDB 4BIM · PDBe 4BIM · UniProt Q9C169
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