Research workbench
Crystal structure of msm DNAB1 intein splicing domain bound with zinc
Analyse Crystal structure of msm DNAB1 intein splicing domain bound with zinc in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OWN
- Type
- protein
- Length
- 381 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Replicative DNA helicase
- EC
- 3.6.4.12
- UniProt
- A0A0D6J385
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Replicative DNA helicase (EC 3.6.4.12) | protein | 127 | 2% helix, 50% strand | A0A0D6J385 |
| B | Replicative DNA helicase (EC 3.6.4.12) | protein | 129 | 2% helix, 53% strand | A0A0D6J385 |
| C | Replicative DNA helicase (EC 3.6.4.12) | protein | 125 | 2% helix, 51% strand | A0A0D6J385 |
Ligands and binding sites
- ZN · Zinc ion · metal · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 600 | 0.63 | 0.74 | 67 | empty |
Interfaces
3 interfaces between chains.
- A–C · 373 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 211 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 50 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6OWN · Crystal structure of Msm DnaB1 intein splicing domain bound with zinc · 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 A0A0D6J385
- Elsewhere: RCSB PDB 6OWN · PDBe 6OWN · UniProt A0A0D6J385
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