MolNFT v1 · #183059 · protein
Crystal structure of ZC3H12C pin catalytic mutant
7NDK · Probable ribonuclease ZC3H12C: “Crystal structure of ZC3H12C pin catalytic mutant”. X-ray diffraction, 1 ligand (NA), 6 pockets (best druggability 0.76). MolNFT v1 #183059 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7NDK
- Type
- protein
- Length
- 623 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable ribonuclease ZC3H12C
- EC
- 3.1.-.-
- UniProt
- Q5DTV4
- Ligands
- NA
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable ribonuclease ZC3H12C (EC 3.1.-.-) | protein | 155 | 40% helix, 23% strand | Q5DTV4 |
| B | Probable ribonuclease ZC3H12C (EC 3.1.-.-) | protein | 153 | 41% helix, 23% strand | Q5DTV4 |
| C | Probable ribonuclease ZC3H12C (EC 3.1.-.-) | protein | 156 | 38% helix, 21% strand | Q5DTV4 |
| D | Probable ribonuclease ZC3H12C (EC 3.1.-.-) | protein | 159 | 38% helix, 19% strand | Q5DTV4 |
Ligands and binding sites
- NA · Sodium ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1109 | 0.76 | 0.79 | 82 | empty |
| 2 | 247 | 0.60 | 0.80 | 32 | empty |
| 3 | 77 | 0.36 | 0.76 | 16 | empty |
| 4 | 68 | 0.33 | 0.76 | 16 | empty |
| 5 | 54 | 0.29 | 0.76 | 16 | empty |
Interfaces
4 interfaces between chains.
- B–C · 1187 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1053 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 417 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 403 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
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 Q5DTV4
- Elsewhere: RCSB PDB 7NDK · PDBe 7NDK · UniProt Q5DTV4
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