Research workbench
Crystal structure of maze-mazf (form-II) from deinococcus radiodurans
Analyse Crystal structure of maze-mazf (form-II) from deinococcus radiodurans in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D2P
- Type
- protein
- Length
- 489 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoribonuclease mazf; ABRB/MAZE/SPOVT family DNA-binding domain-containing protein
- EC
- 3.1.27.-
- UniProt
- A0A6G9BVQ8, A0A6G9BVE7
- Pockets
- 3 · best druggability 0.38
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Endoribonuclease mazf (EC 3.1.27.-) | protein | 111 | 25% helix, 34% strand | A0A6G9BVQ8 |
| C | Endoribonuclease mazf (EC 3.1.27.-) | protein | 104 | 23% helix, 34% strand | A0A6G9BVQ8 |
| D | Endoribonuclease mazf (EC 3.1.27.-) | protein | 103 | 23% helix, 32% strand | A0A6G9BVQ8 |
| E, F | ABRB/MAZE/SPOVT family DNA-binding domain-containing protein | protein | 30 | 20% helix, 3% strand | A0A6G9BVE7 |
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 | 79 | 0.38 | 0.77 | 18 | empty |
| 2 | 50 | 0.35 | 0.79 | 20 | empty |
| 3 | 67 | 0.33 | 0.76 | 17 | empty |
Interfaces
7 interfaces between chains.
- A–E · 1269 Ų buried · 17 hydrogen bonds · protein-protein
- B–F · 1260 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 890 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 874 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 649 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7D2P · Crystal structure of MazE-MazF (Form-II) from Deinococcus radiodurans · 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 A0A6G9BVQ8
- Every structure of UniProt A0A6G9BVE7
- Elsewhere: RCSB PDB 7D2P · PDBe 7D2P · UniProt A0A6G9BVQ8 · UniProt A0A6G9BVE7
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