MolNFT v1 · #47680 · protein
Crystal structure of the poplar glutathione peroxidase 5 in the reduced form
2P5Q: “Crystal structure of the poplar glutathione peroxidase 5 in the reduced form”. X-ray diffraction, 1 ligand (CD), 4 pockets (best druggability 0.55). MolNFT v1 #47680 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2P5Q
- Type
- protein
- Length
- 641 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutathione peroxidase 5
- EC
- 1.11.1.-
- UniProt
- A3FNZ8
- Ligands
- CD
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutathione peroxidase 5 (EC 1.11.1.-) | protein | 161 | 36% helix, 21% strand | A3FNZ8 |
| B, C, D | Glutathione peroxidase 5 (EC 1.11.1.-) | protein | 160 | 36% helix, 21% strand | A3FNZ8 |
Ligands and binding sites
- CD · Cadmium ion · metal · 32 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 393 | 0.55 | 0.74 | 50 | CD |
| 2 | 290 | 0.50 | 0.73 | 37 | CD |
| 3 | 93 | 0.35 | 0.74 | 21 | CD |
| 4 | 79 | 0.32 | 0.74 | 19 | CD |
Interfaces
3 interfaces between chains.
- A–B · 857 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 852 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 652 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2P5Q · Crystal structure of the poplar glutathione peroxidase 5 in the reduced form · the same entry in another collection · 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 A3FNZ8
- Elsewhere: RCSB PDB 2P5Q · PDBe 2P5Q · UniProt A3FNZ8
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