MolNFT v1 · #171364 · protein
Toprim domain of RNase M5 bound with two MG2+ ions
6Z2B · Ribonuclease M5: “Toprim domain of RNase M5 bound with two MG2+ ions”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.47). MolNFT v1 #171364 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6Z2B
- Type
- protein
- Length
- 420 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonuclease M5
- EC
- 3.1.26.8
- UniProt
- A0A087LGV4
- Ligands
- MG
- Pockets
- 4 · best druggability 0.47
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonuclease M5 (EC 3.1.26.8) | protein | 102 | 45% helix, 12% strand | A0A087LGV4 |
| B | Ribonuclease M5 (EC 3.1.26.8) | protein | 114 | 46% helix, 15% strand | A0A087LGV4 |
| C | Ribonuclease M5 (EC 3.1.26.8) | protein | 102 | 45% helix, 15% strand | A0A087LGV4 |
| D | Ribonuclease M5 (EC 3.1.26.8) | protein | 102 | 48% helix, 14% strand | A0A087LGV4 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 113 | 0.47 | 0.79 | 25 | empty |
| 2 | 92 | 0.39 | 0.77 | 17 | empty |
| 3 | 91 | 0.38 | 0.76 | 17 | empty |
| 4 | 50 | 0.25 | 0.73 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 694 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 514 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 486 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6Z2B · Toprim domain of RNase M5 bound with two Mg2+ ions · 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 A0A087LGV4
- Elsewhere: RCSB PDB 6Z2B · PDBe 6Z2B · UniProt A0A087LGV4
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