MolNFT v1 · #182551 · protein + RNA
Crystal structure analysis of xac nucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE
7MW8 · Phosphodiesterase-nucleotide pyrophosphatase: “Crystal structure analysis of xac nucleotide PYROPHOSPHATASE/PHOSPHODIESTERASE”. X-ray diffraction, 1 ligand (ZN), 17 pockets (best druggability 0.83). MolNFT v1 #182551 on GenesisL1…
- PDB
- 7MW8
- Type
- protein + RNA
- Length
- 2,307 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphodiesterase-nucleotide pyrophosphatase; Papg
- UniProt
- A0A0U5FM15
- Ligands
- ZN
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 7 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | Phosphodiesterase-nucleotide pyrophosphatase | protein | 383 | 33% helix, 22% strand | A0A0U5FM15 |
| B, E | Phosphodiesterase-nucleotide pyrophosphatase | protein | 384 | 34% helix, 22% strand | A0A0U5FM15 |
| C | Phosphodiesterase-nucleotide pyrophosphatase | protein | 385 | 33% helix, 22% strand | A0A0U5FM15 |
| A | Phosphodiesterase-nucleotide pyrophosphatase | protein | 380 | 34% helix, 23% strand | A0A0U5FM15 |
| F | Phosphodiesterase-nucleotide pyrophosphatase | protein | 384 | 34% helix, 22% strand | A0A0U5FM15 |
| J | Papg | rna | 2 | — | — |
| K, L, M, N, O | Papg | rna | 1 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 12 copies · chains D, K, B, L, C, M, A, J, E, N, F, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1197 | 0.83 | 0.84 | 114 | empty |
| 2 | 966 | 0.83 | 0.84 | 112 | empty |
| 3 | 1095 | 0.81 | 0.83 | 105 | empty |
| 4 | 1116 | 0.80 | 0.82 | 118 | empty |
| 5 | 387 | 0.59 | 0.76 | 38 | empty |
Interfaces
14 interfaces between chains.
- B–E · 625 Ų buried · 10 hydrogen bonds · protein-protein
- D–A · 617 Ų buried · 1 hydrogen bond · protein-protein
- C–F · 617 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 597 Ų buried · 14 hydrogen bonds · protein-protein
- A–J · 561 Ų buried · 15 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7MW8 · Crystal Structure Analysis of Xac Nucleotide Pyrophosphatase/Phosphodiesterase · the same entry in another collection · chain D against D, 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 A0A0U5FM15
- Elsewhere: RCSB PDB 7MW8 · PDBe 7MW8 · UniProt A0A0U5FM15
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