MolNFT v1 · #120605 · protein
Crystal structure of human GPX4 in complex with gxpep-1
5H5Q · Phospholipid hydroperoxide glutathione peroxidase…: “Crystal structure of human GPX4 in complex with gxpep-1”. X-ray diffraction, 2 ligands (ACE, NH2), 1 pocket (best druggability 0.29). MolNFT v1 #120605 on GenesisL1: 3D structure…
- PDB
- 5H5Q
- Type
- protein
- Length
- 178 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phospholipid hydroperoxide glutathione peroxidase, mitochondrial; Gxpep-1
- EC
- 1.11.1.12
- UniProt
- P36969
- Ligands
- ACE, NH2
- Pockets
- 1 · best druggability 0.29
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phospholipid hydroperoxide glutathione peroxidase, mitochondrial (EC 1.11.1.12) | protein | 165 | 33% helix, 19% strand | P36969 |
| B | Gxpep-1 | protein | 13 | 0% helix, 38% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains B
- NH2 · Amino group · ion · chains B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.29 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 527 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 disulfide, 1 modified (covalent ligand, disulfide, oxidation).
Compared structures
- 5H5Q · Crystal structure of human GPX4 in complex with GXpep-1 · 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 P36969
- Elsewhere: RCSB PDB 5H5Q · PDBe 5H5Q · UniProt P36969
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