MolNFT v1 · #185233 · protein
Crystal structure of the parp domain of wheat SRO1
7PLQ · Similar to RCD1 (SRO1): “Crystal structure of the parp domain of wheat SRO1”. X-ray diffraction, 2 ligands (P4G, SO4), 5 pockets (best druggability 0.56). MolNFT v1 #185233 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7PLQ
- Type
- protein
- Length
- 361 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Similar to RCD1 (SRO1)
- UniProt
- A0A3B6LXD6
- Ligands
- P4G, SO4
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Similar to RCD1 (SRO1) | protein | 178 | 29% helix, 28% strand | A0A3B6LXD6 |
| B | Similar to RCD1 (SRO1) | protein | 183 | 27% helix, 28% strand | A0A3B6LXD6 |
Ligands and binding sites
- P4G · 1-ethoxy-2-(2-ethoxyethoxy)ethane · ligand · chains B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 140 | 0.56 | 0.82 | 20 | empty |
| 2 | 140 | 0.55 | 0.82 | 20 | empty |
| 3 | 165 | 0.50 | 0.78 | 32 | EDO |
| 4 | 91 | 0.48 | 0.82 | 22 | empty |
| 5 | 80 | 0.47 | 0.82 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1169 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 19 modified (engineered).
Compared structures
- 7PLQ · Crystal structure of the PARP domain of wheat SRO1 · 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 A0A3B6LXD6
- Elsewhere: RCSB PDB 7PLQ · PDBe 7PLQ · UniProt A0A3B6LXD6
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