Research workbench
Truncated xpd
Analyse Truncated xpd in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H8C
- Type
- protein
- Length
- 335 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- XPD/RAD3 related DNA helicase
- UniProt
- M1J2P5
- Ligands
- SF4
- Pockets
- 5 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | XPD/RAD3 related DNA helicase | protein | 335 | 49% helix, 14% strand | M1J2P5 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 210 | 0.50 | 0.76 | 29 | empty |
| 2 | 110 | 0.46 | 0.79 | 25 | empty |
| 3 | 73 | 0.44 | 0.81 | 14 | empty |
| 4 | 162 | 0.43 | 0.74 | 20 | empty |
| 5 | 51 | 0.36 | 0.79 | 15 | empty |
Compared structures
- 5H8C · Truncated XPD · 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 M1J2P5
- Elsewhere: RCSB PDB 5H8C · PDBe 5H8C · UniProt M1J2P5
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