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Crystal structure of M. tuberculosis mazf-MT3 T52D-F62D mutant in complex with 8-mer RNA
Analyse Crystal structure of M. tuberculosis mazf-MT3 T52D-F62D mutant in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HKC
- Type
- protein + RNA
- Length
- 228 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoribonuclease MAZF6; RNA (5'-R(*GP*UP*C)-D(P*U)-R(P*CP*CP*UP*A)-3')
- EC
- 3.1.27.-
- UniProt
- P9WII2
- Pockets
- 2 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 27% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoribonuclease MAZF6 (EC 3.1.27.-) | protein | 114 | 28% helix, 36% strand | P9WII2 |
| B | Endoribonuclease MAZF6 (EC 3.1.27.-) | protein | 112 | 26% helix, 40% strand | P9WII2 |
| C | RNA (5'-R(*GP*UP*C)-D(P*U)-R(P*CP*CP*UP*A)-3') | rna | 2 | — | — |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.57 | 0.75 | 36 | empty |
| 2 | 110 | 0.42 | 0.77 | 21 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1217 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 370 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 5HKC · Crystal structure of M. tuberculosis MazF-mt3 T52D-F62D mutant in complex with 8-mer RNA · the same entry in another collection · chain A against A, TM-score 1.00
- P9WII2 · AlphaFold monomer V2.0 prediction for endoribonuclease MAZF6 (P9WII2) · a predicted model of the same protein · 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 P9WII2
- Elsewhere: RCSB PDB 5HKC · PDBe 5HKC · UniProt P9WII2
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