Research workbench
E. COLI mazf in complex with single strand DNA substrate analog
Analyse E. COLI mazf in complex with single strand DNA substrate analog in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CR2
- Type
- protein + DNA
- Length
- 336 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoribonuclease mazf; Ssdna substrate analog
- EC
- 3.1.27.-
- UniProt
- P0AE70
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 5 distinct chains · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoribonuclease mazf (EC 3.1.27.-) | protein | 111 | 23% helix, 33% strand | P0AE70 |
| B | Endoribonuclease mazf (EC 3.1.27.-) | protein | 108 | 23% helix, 31% strand | P0AE70 |
| C | Endoribonuclease mazf (EC 3.1.27.-) | protein | 110 | 19% helix, 32% strand | P0AE70 |
| D | Ssdna substrate analog | dna | 5 | — | — |
| E, F | Ssdna substrate analog | dna | 1 | — | — |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.71 | 0.97 | 18 | empty |
| 2 | 81 | 0.41 | 0.78 | 14 | empty |
| 3 | 81 | 0.36 | 0.76 | 15 | empty |
| 4 | 103 | 0.33 | 0.73 | 25 | empty |
| 5 | 77 | 0.32 | 0.75 | 15 | empty |
Interfaces
7 interfaces between chains.
- A–B · 1187 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 651 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–E · 240 Ų buried · 2 hydrogen bonds · protein-nucleic
- C–F · 234 Ų buried · 3 hydrogen bonds · protein-nucleic
- B–C · 164 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5CR2 · E. coli MazF in complex with single strand DNA substrate analog · the same entry in another collection · chain A against A, TM-score 1.00
- P0AE70 · AlphaFold monomer V2.0 prediction for endoribonuclease toxin mazf (P0AE70) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P0AE70
- Elsewhere: RCSB PDB 5CR2 · PDBe 5CR2 · UniProt P0AE70
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