Research workbench
Crystal structure of the intermembrane space region of the plastid division protein PARC6
Analyse Crystal structure of the intermembrane space region of the plastid division… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U9L
- Type
- protein
- Length
- 303 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Paralog of accumulation and replication of chloroplasts 6 (PARC6)
- UniProt
- Q8VY16
- Ligands
- MG
- Pockets
- 2 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Paralog of accumulation and replication of chloroplasts 6 (PARC6) | protein | 152 | 32% helix, 43% strand | Q8VY16 |
| B | Paralog of accumulation and replication of chloroplasts 6 (PARC6) | protein | 151 | 32% helix, 45% strand | Q8VY16 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 88 | 0.46 | 0.81 | 29 | empty |
| 2 | 62 | 0.29 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 992 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5U9L · Crystal structure of the intermembrane space region of the plastid division protein PARC6 · the same entry in another collection · chain A against A, TM-score 1.00
- Q8VY16 · AlphaFold monomer V2.0 prediction for plastid division protein CDP1, chloroplastic… · a predicted model of the same protein · chain B against A, TM-score 0.87
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 Q8VY16
- Elsewhere: RCSB PDB 5U9L · PDBe 5U9L · UniProt Q8VY16
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