MolNFT v1 · #109644 · protein
Crystal structure of human PGRMC1 cytochrome B5-like domain
4X8Y · Membrane-associated progesterone receptor component 1: “Crystal structure of human PGRMC1 cytochrome B5-like domain”. X-ray diffraction, 1 ligand (HEM), 4 pockets (best druggability 0.51). MolNFT v1 #109644 on GenesisL1: 3D…
- PDB
- 4X8Y
- Type
- protein
- Length
- 222 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Membrane-associated progesterone receptor component 1
- UniProt
- O00264
- Ligands
- HEM
- Pockets
- 4 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Membrane-associated progesterone receptor component 1 | protein | 112 | 38% helix, 16% strand | O00264 |
| B | Membrane-associated progesterone receptor component 1 | protein | 110 | 39% helix, 16% strand | O00264 |
Ligands and binding sites
- HEM · Protoporphyrin IX containing Fe · ligand · 2 copies · chains A, B
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 | 109 | 0.51 | 0.81 | 19 | HEM |
| 2 | 71 | 0.38 | 0.77 | 14 | HEM |
| 3 | 54 | 0.34 | 0.78 | 13 | empty |
| 4 | 52 | 0.29 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 549 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4X8Y · Crystal structure of human PGRMC1 cytochrome b5-like domain · the same entry in another collection · chain A against A, TM-score 1.00
- O00264 · AlphaFold monomer V2.0 prediction for membrane-associated progesterone receptor component… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O00264
- Elsewhere: RCSB PDB 4X8Y · PDBe 4X8Y · UniProt O00264
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