MolNFT v1 · #28437 · protein
Crystal structure of proteolytically truncated catalase hpii from E. COLI
1YE9: “Crystal structure of proteolytically truncated catalase hpii from E. COLI”. X-ray diffraction, 1 ligand (HDD), 20 pockets (best druggability 0.89). MolNFT v1 #28437 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1YE9
- Type
- protein
- Length
- 3,832 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Catalase hpii
- EC
- 1.11.1.6
- UniProt
- P21179
- Ligands
- HDD
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, I, J, K, L | Catalase hpii (EC 1.11.1.6) | protein | 223 | 22% helix, 28% strand | P21179 |
| E, F, G, H, M, N, O, P | Catalase hpii (EC 1.11.1.6) | protein | 256 | 38% helix, 13% strand | P21179 |
Ligands and binding sites
- HDD · Cis-heme D hydroxychlorin gamma-spirolactone · ligand · 8 copies · chains A, E, D, B, F, C, G, H, I, M, L, J, N, K, O, P
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 | 500 | 0.89 | 0.96 | 60 | empty |
| 2 | 500 | 0.89 | 0.96 | 62 | empty |
| 3 | 483 | 0.89 | 0.96 | 60 | empty |
| 4 | 491 | 0.88 | 0.96 | 56 | empty |
| 5 | 301 | 0.86 | 0.96 | 53 | HDD |
Interfaces
56 interfaces between chains.
- D–H · 5551 Ų buried · 97 hydrogen bonds · protein-protein
- J–N · 5546 Ų buried · 97 hydrogen bonds · protein-protein
- I–M · 5537 Ų buried · 98 hydrogen bonds · protein-protein
- B–F · 5537 Ų buried · 97 hydrogen bonds · protein-protein
- A–E · 5517 Ų buried · 95 hydrogen bonds · protein-protein
Compared structures
- 1YE9 · Crystal structure of proteolytically truncated catalase HPII from E. coli · the same entry in another collection · chain M against M, 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 P21179
- Elsewhere: RCSB PDB 1YE9 · PDBe 1YE9 · UniProt P21179
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