MolNFT v1 · #116739 · protein
Structure of the nhej polymerase from methanocella paludicola
5DMU: “Structure of the nhej polymerase from methanocella paludicola”. X-ray diffraction, 2 ligands (NA, SO4), 3 pockets (best druggability 0.36). MolNFT v1 #116739 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5DMU
- Type
- protein
- Length
- 301 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nhej polymerase
- UniProt
- D1Z0H5
- Ligands
- NA, SO4
- Pockets
- 3 · best druggability 0.36
Structure
x-ray diffraction · 1 distinct chain · 27% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nhej polymerase | protein | 301 | 27% helix, 26% strand | D1Z0H5 |
Ligands and binding sites
- NA · Sodium ion · metal · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 78 | 0.36 | 0.76 | 14 | empty |
| 2 | 61 | 0.31 | 0.76 | 13 | empty |
| 3 | 54 | 0.28 | 0.74 | 13 | EDO |
Compared structures
- 5DMU · Structure of the NHEJ polymerase from Methanocella paludicola · 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 D1Z0H5
- Elsewhere: RCSB PDB 5DMU · PDBe 5DMU · UniProt D1Z0H5
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