MolNFT v1 · #162889 · protein
Structure of ATP bound plasmodium falciparum imp-nucleotidase
6RMD · Imp-specific 5'-nucleotidase, putative: “Structure of ATP bound plasmodium falciparum imp-nucleotidase”. X-ray diffraction, 1 ligand (ATP), 9 pockets (best druggability 0.80). MolNFT v1 #162889 on GenesisL1: 3D structure, binding…
- PDB
- 6RMD
- Type
- protein
- Length
- 797 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Imp-specific 5'-nucleotidase, putative
- EC
- 3.1.3.5
- UniProt
- A0A144A134
- Ligands
- ATP
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Imp-specific 5'-nucleotidase, putative (EC 3.1.3.5) | protein | 425 | 47% helix, 12% strand | A0A144A134 |
| D | Imp-specific 5'-nucleotidase, putative (EC 3.1.3.5) | protein | 372 | 49% helix, 15% strand | A0A144A134 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains D
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1042 | 0.80 | 0.81 | 94 | EDO |
| 2 | 201 | 0.73 | 0.89 | 29 | empty |
| 3 | 396 | 0.67 | 0.80 | 56 | empty |
| 4 | 229 | 0.52 | 0.76 | 32 | empty |
| 5 | 102 | 0.45 | 0.79 | 15 | ATP |
Interfaces
1 interface between chains.
- A–D · 1000 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 6RMD · Structure of ATP bound Plasmodium falciparum IMP-nucleotidase · 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 A0A144A134
- Elsewhere: RCSB PDB 6RMD · PDBe 6RMD · UniProt A0A144A134
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