MolNFT v1 · #74883 · protein
Structure of I274A variant of E. COLI kate
3P9S · Catalase hpii: “Structure of I274A variant of E. COLI kate”. X-ray diffraction, 2 ligands (HDD, HDE), 20 pockets (best druggability 0.89). MolNFT v1 #74883 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3P9S
- Type
- protein
- Length
- 2,904 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalase hpii
- EC
- 1.11.1.6
- UniProt
- P21179
- Ligands
- HDD, HDE
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Catalase hpii (EC 1.11.1.6) | protein | 726 | 32% helix, 18% strand | P21179 |
Ligands and binding sites
- HDD · Cis-heme D hydroxychlorin gamma-spirolactone · ligand · 4 copies · chains A, D, B, C
- HDE · Cis-heme D hydroxychlorin gamma-spirolactone 17R, 18S · ligand · 4 copies · chains A, D, 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 483 | 0.89 | 0.96 | 59 | empty |
| 2 | 485 | 0.88 | 0.96 | 57 | empty |
| 3 | 365 | 0.86 | 0.95 | 44 | empty |
| 4 | 290 | 0.85 | 0.96 | 52 | HDD, HDE |
| 5 | 270 | 0.84 | 0.95 | 43 | HDD, HDE |
Interfaces
6 interfaces between chains.
- A–D · 6245 Ų buried · 116 hydrogen bonds · protein-protein
- B–C · 6233 Ų buried · 116 hydrogen bonds · protein-protein
- B–D · 5926 Ų buried · 81 hydrogen bonds · protein-protein
- A–C · 5881 Ų buried · 80 hydrogen bonds · protein-protein
- C–D · 2290 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
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 P21179
- Elsewhere: RCSB PDB 3P9S · PDBe 3P9S · UniProt P21179
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