MolNFT v1 · #8568 · protein
Monoclinic form of human peroxiredoxin 5
1H4O: “Monoclinic form of human peroxiredoxin 5”. X-ray diffraction, 1 ligand (BEZ), 13 pockets (best druggability 0.59). MolNFT v1 #8568 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1H4O
- Type
- protein
- Length
- 1,288 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxiredoxin 5
- EC
- 1.11.1.15
- UniProt
- P30044
- Ligands
- BEZ
- Pockets
- 13 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Peroxiredoxin 5 (EC 1.11.1.15) | protein | 161 | 29% helix, 25% strand | P30044 |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 257 | 0.59 | 0.79 | 45 | BEZ |
| 2 | 293 | 0.58 | 0.78 | 52 | BEZ |
| 3 | 139 | 0.50 | 0.79 | 25 | BEZ |
| 4 | 104 | 0.50 | 0.81 | 20 | BEZ |
| 5 | 138 | 0.49 | 0.78 | 27 | BEZ |
Interfaces
6 interfaces between chains.
- B–C · 465 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 459 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 450 Ų buried · 5 hydrogen bonds · protein-protein
- F–G · 446 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 305 Ų buried · 4 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 P30044
- Elsewhere: RCSB PDB 1H4O · PDBe 1H4O · UniProt P30044
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