MolNFT v1 · #79353 · protein
Crystal structure of a putative DNA polymerase III beta subunit (EUBREC_0002; ERE_29750) from eubacterium rectale atcc 33656 at 2.26 a resolution
3T0P · DNA polymerase III, beta subunit: “Crystal structure of a putative DNA polymerase III beta subunit (EUBREC_0002; ERE_29750) from eubacterium…”. X-ray diffraction, 1 ligand (CL), 2 pockets (best druggability 0.34). MolNFT v1 #79353…
- PDB
- 3T0P
- Type
- protein
- Length
- 733 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase III, beta subunit
- UniProt
- C4Z938
- Ligands
- CL
- Pockets
- 2 · best druggability 0.34
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase III, beta subunit | protein | 365 | 22% helix, 45% strand | C4Z938 |
| B | DNA polymerase III, beta subunit | protein | 368 | 21% helix, 45% strand | C4Z938 |
Ligands and binding sites
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 18 copies · chains A, B
- ACT · Acetate ion · additive · 5 copies · chains A, B
- PGR · R-1,2-propanediol · additive · 2 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.34 | 0.74 | 17 | ACT |
| 2 | 53 | 0.30 | 0.76 | 10 | empty |
Interfaces
1 interface between chains.
- A–B · 1255 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 3T0P · Crystal structure of a Putative DNA polymerase III beta subunit (EUBREC_0002; ERE_29750)… · 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 C4Z938
- Elsewhere: RCSB PDB 3T0P · PDBe 3T0P · UniProt C4Z938
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