Research workbench
Crystal structure of WHY1 from arabidopsis thaliana
Analyse Crystal structure of WHY1 from arabidopsis thaliana in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KOO
- Type
- protein
- Length
- 678 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Single-stranded DNA-binding protein WHY1, chloroplastic
- UniProt
- Q9M9S3
- Ligands
- NI, PO4
- Pockets
- 9 · best druggability 0.60
Structure
x-ray diffraction · 4 distinct chains · 22% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Single-stranded DNA-binding protein WHY1, chloroplastic | protein | 176 | 22% helix, 40% strand | Q9M9S3 |
| B | Single-stranded DNA-binding protein WHY1, chloroplastic | protein | 162 | 20% helix, 43% strand | Q9M9S3 |
| C | Single-stranded DNA-binding protein WHY1, chloroplastic | protein | 165 | 19% helix, 43% strand | Q9M9S3 |
| D | Single-stranded DNA-binding protein WHY1, chloroplastic | protein | 175 | 25% helix, 41% strand | Q9M9S3 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · chains A
- PO4 · Phosphate ion · ion · chains B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 6 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 403 | 0.60 | 0.76 | 53 | empty |
| 2 | 271 | 0.53 | 0.75 | 42 | empty |
| 3 | 295 | 0.52 | 0.74 | 35 | empty |
| 4 | 136 | 0.48 | 0.79 | 24 | empty |
| 5 | 122 | 0.41 | 0.75 | 21 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1591 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1208 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 245 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 226 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 183 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
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 Q9M9S3
- Elsewhere: RCSB PDB 4KOO · PDBe 4KOO · UniProt Q9M9S3
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