Research workbench
Structure of S. tokodaii XPD4
Analyse Structure of S. tokodaii XPD4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VL7
- Type
- protein
- Length
- 459 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Xpd
- UniProt
- Q971R4
- Ligands
- PO4
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Xpd | protein | 459 | 46% helix, 18% strand | Q971R4 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.58 | 0.80 | 37 | empty |
| 2 | 365 | 0.58 | 0.75 | 42 | empty |
| 3 | 136 | 0.44 | 0.77 | 18 | PO4 |
| 4 | 56 | 0.35 | 0.77 | 15 | empty |
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 2VL7 · Structure of S. tokodaii Xpd4 · 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 Q971R4
- Elsewhere: RCSB PDB 2VL7 · PDBe 2VL7 · UniProt Q971R4
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