Research workbench
Catalase 3 from N.CRASSA in ferrous state, X-ray reduced (1.315 mgy)
Analyse Catalase 3 from N.CRASSA in ferrous state, X-ray reduced (1.315 mgy) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NT0
- Type
- protein
- Length
- 2,716 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 0.86
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Catalase-3 (EC 1.11.1.6) | protein | 682 | 33% helix, 18% strand | Q9C169 |
| B | Catalase-3 (EC 1.11.1.6) | protein | 677 | 33% helix, 18% strand | Q9C169 |
| C | Catalase-3 (EC 1.11.1.6) | protein | 679 | 32% helix, 18% strand | Q9C169 |
| D | Catalase-3 (EC 1.11.1.6) | protein | 678 | 33% helix, 17% strand | Q9C169 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 4 copies · chains A, D, B, C
- ACT · Acetate ion · additive · 8 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C, D
- EOH · Ethanol · additive · 7 copies · chains A, B, D
- PEG · Di(hydroxyethyl)ether · additive · 5 copies · chains A, B, C
- PGE · Triethylene glycol · additive · 4 copies · chains A, B, C, D
- PG4 · Tetraethylene glycol · additive · chains C
- P6G · Hexaethylene glycol · additive · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 270 | 0.86 | 0.97 | 48 | HEM, ACT |
| 2 | 281 | 0.85 | 0.96 | 48 | HEM, ACT |
| 3 | 256 | 0.85 | 0.96 | 45 | HEM, ACT |
| 4 | 986 | 0.84 | 0.85 | 115 | PGE |
| 5 | 233 | 0.83 | 0.95 | 37 | HEM |
Interfaces
6 interfaces between chains.
- A–D · 5950 Ų buried · 93 hydrogen bonds · protein-protein
- B–C · 5802 Ų buried · 94 hydrogen bonds · protein-protein
- A–C · 5078 Ų buried · 70 hydrogen bonds · protein-protein
- B–D · 5060 Ų buried · 71 hydrogen bonds · protein-protein
- A–B · 2289 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
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 6NT0 · PDBe 6NT0 · UniProt Q9C169
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