MolNFT v1 · #136826 · protein
Crystal structure of mppr-1I soaked with selenourea for 10 min
5V51 · Pr-1 protein: “Crystal structure of mppr-1I soaked with selenourea for 10 min”. X-ray diffraction, 1 ligand (SEY), 5 pockets (best druggability 0.52). MolNFT v1 #136826 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5V51
- Type
- protein
- Length
- 924 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pr-1 protein
- UniProt
- H6U756
- Ligands
- SEY
- Pockets
- 5 · best druggability 0.52
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, G | Pr-1 protein | protein | 132 | 44% helix, 22% strand | H6U756 |
| C | Pr-1 protein | protein | 127 | 40% helix, 18% strand | H6U756 |
| D | Pr-1 protein | protein | 132 | 43% helix, 19% strand | H6U756 |
| F | Pr-1 protein | protein | 137 | 41% helix, 20% strand | H6U756 |
Ligands and binding sites
- SEY · selenourea · ligand · 9 copies · chains A, B, C, D, E, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.52 | 0.84 | 21 | SEY |
| 2 | 68 | 0.51 | 0.85 | 20 | SEY |
| 3 | 79 | 0.47 | 0.82 | 21 | SEY |
| 4 | 62 | 0.47 | 0.84 | 20 | SEY |
| 5 | 54 | 0.36 | 0.79 | 13 | SEY |
Interfaces
6 interfaces between chains.
- E–F · 840 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 834 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 830 Ų buried · 10 hydrogen bonds · protein-protein
- F–G · 816 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 804 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide (disulfide).
Compared structures
- 5V51 · Crystal Structure of MpPR-1i Soaked with Selenourea for 10 min · 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 H6U756
- Elsewhere: RCSB PDB 5V51 · PDBe 5V51 · UniProt H6U756
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