MolNFT v1 · #135896 · protein
The structure of archaeal inorganic pyrophosphatase in complex with pyrophosphate
5UCQ: “The structure of archaeal inorganic pyrophosphatase in complex with pyrophosphate”. X-ray diffraction, 3 ligands (POP, CA, NA), 5 pockets (best druggability 0.82). MolNFT v1 #135896 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5UCQ
- Type
- protein
- Length
- 526 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inorganic pyrophosphatase
- EC
- 3.6.1.1
- UniProt
- H0USY5
- Ligands
- POP, CA, NA
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 175 | 26% helix, 35% strand | H0USY5 |
| B | Inorganic pyrophosphatase (EC 3.6.1.1) | protein | 176 | 25% helix, 35% strand | H0USY5 |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 3 copies · chains A, B, C
- CA · Calcium ion · metal · 9 copies · chains A, B, C
- NA · Sodium ion · metal · chains B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C
- MRD · (4R)-2-methylpentane-2,4-diol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.82 | 0.92 | 32 | EDO |
| 2 | 139 | 0.50 | 0.79 | 25 | CA, EDO, POP, NA |
| 3 | 129 | 0.48 | 0.79 | 26 | CA, POP |
| 4 | 131 | 0.47 | 0.78 | 25 | CA, POP |
| 5 | 90 | 0.33 | 0.73 | 26 | EDO |
Interfaces
3 interfaces between chains.
- A–C · 832 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 818 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 779 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5UCQ · The structure of archaeal Inorganic Pyrophosphatase in complex with pyrophosphate · 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 H0USY5
- Elsewhere: RCSB PDB 5UCQ · PDBe 5UCQ · UniProt H0USY5
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