MolNFT v1 · #139384 · protein
Endoribonuclease in complex with its cognate antitoxin from mycobacterial species
5XE3 · Endoribonuclease MAZF4: “Endoribonuclease in complex with its cognate antitoxin from mycobacterial species”. X-ray diffraction, 6 pockets (best druggability 0.53). MolNFT v1 #139384 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5XE3
- Type
- protein
- Length
- 568 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoribonuclease MAZF4; Probable antitoxin MAZE4
- EC
- 3.1.-.-
- UniProt
- P9WII5, P9WJ91
- Pockets
- 6 · best druggability 0.53
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | Endoribonuclease MAZF4 (EC 3.1.-.-) | protein | 103 | 22% helix, 37% strand | P9WII5 |
| D, B | Endoribonuclease MAZF4 (EC 3.1.-.-) | protein | 100 | 23% helix, 37% strand | P9WII5 |
| F, E | Probable antitoxin MAZE4 | protein | 81 | 75% helix, 1% strand | P9WJ91 |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.53 | 0.75 | 47 | empty |
| 2 | 314 | 0.52 | 0.74 | 34 | empty |
| 3 | 76 | 0.41 | 0.79 | 17 | empty |
| 4 | 80 | 0.36 | 0.76 | 16 | empty |
| 5 | 61 | 0.31 | 0.75 | 11 | empty |
Interfaces
10 interfaces between chains.
- F–E · 1319 Ų buried · 20 hydrogen bonds · protein-protein
- A–E · 949 Ų buried · 17 hydrogen bonds · protein-protein
- C–F · 941 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 814 Ų buried · 16 hydrogen bonds · protein-protein
- D–F · 812 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5XE3 · Endoribonuclease in complex with its cognate antitoxin from Mycobacterial species · the same entry in another collection · chain E against E, TM-score 1.00
- P9WII5 · AlphaFold monomer V2.0 prediction for endoribonuclease MAZF4 (P9WII5) · a predicted model of the same protein · chain C against A, TM-score 0.97
- P9WJ91 · AlphaFold monomer V2.0 prediction for probable antitoxin MAZE4 (P9WJ91) · a predicted model of the same protein · chain F against A, TM-score 0.97
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 P9WII5
- Every structure of UniProt P9WJ91
- Elsewhere: RCSB PDB 5XE3 · PDBe 5XE3 · UniProt P9WII5 · UniProt P9WJ91
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