MolNFT v1 · #121059 · protein + RNA
Crystal structure of M. tuberculosis mazf-MT3 (RV1991C) in complex with RNA
5HK0 · Endoribonuclease MAZF6: “Crystal structure of M. tuberculosis mazf-MT3 (RV1991C) in complex with RNA”. X-ray diffraction, 4 pockets (best druggability 0.58). MolNFT v1 #121059 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5HK0
- Type
- protein + RNA
- Length
- 433 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endoribonuclease MAZF6; RNA (5'-R(*AP*GP*UP*C)-D(P*U)-R(P*CP*CP*UP*UP*UP*C)-3')
- EC
- 3.1.27.-
- UniProt
- P9WII3
- Pockets
- 4 · best druggability 0.58
Structure
x-ray diffraction · 6 distinct chains · 26% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endoribonuclease MAZF6 (EC 3.1.27.-) | protein | 109 | 27% helix, 39% strand | P9WII3 |
| B | Endoribonuclease MAZF6 (EC 3.1.27.-) | protein | 107 | 29% helix, 39% strand | P9WII3 |
| C | Endoribonuclease MAZF6 (EC 3.1.27.-) | protein | 109 | 23% helix, 36% strand | P9WII3 |
| D | Endoribonuclease MAZF6 (EC 3.1.27.-) | protein | 101 | 27% helix, 37% strand | P9WII3 |
| E | RNA (5'-R(*AP*GP*UP*C)-D(P*U)-R(P*CP*CP*UP*UP*UP*C)-3') | rna | 5 | — | — |
| F | RNA (5'-R(*AP*GP*UP*C)-D(P*U)-R(P*CP*CP*UP*UP*UP*C)-3') | rna | 2 | — | — |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.58 | 0.84 | 27 | empty |
| 2 | 256 | 0.53 | 0.76 | 29 | empty |
| 3 | 175 | 0.43 | 0.73 | 27 | empty |
| 4 | 124 | 0.38 | 0.74 | 24 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1176 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 992 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 582 Ų buried · 5 hydrogen bonds · protein-protein
- B–E · 411 Ų buried · 13 hydrogen bonds · protein-nucleic
- D–F · 354 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 5HK0 · Crystal structure of M. tuberculosis MazF-mt3 (Rv1991c) in complex with RNA · the same entry in another collection · chain E against E, TM-score 1.00
- P9WII3 · AlphaFold monomer V2.0 prediction for endoribonuclease MAZF6 (P9WII3) · a predicted model of the same protein · chain B 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 P9WII3
- Elsewhere: RCSB PDB 5HK0 · PDBe 5HK0 · UniProt P9WII3
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