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Structure of the pr domain from human PRDM5
Analyse Structure of the pr domain from human PRDM5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XAZ
- Type
- protein
- Length
- 243 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pr domain zinc finger protein 5
- EC
- 2.1.1.-
- UniProt
- Q9NQX1
- Pockets
- 2 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pr domain zinc finger protein 5 (EC 2.1.1.-) | protein | 118 | 6% helix, 42% strand | Q9NQX1 |
| B | Pr domain zinc finger protein 5 (EC 2.1.1.-) | protein | 125 | 13% helix, 37% strand | Q9NQX1 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 3 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.53 | 0.78 | 34 | empty |
| 2 | 57 | 0.38 | 0.80 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 981 Ų buried · 10 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 Q9NQX1
- Elsewhere: RCSB PDB 6XAZ · PDBe 6XAZ · UniProt Q9NQX1
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