Research workbench
Structure of imp bound plasmodium falciparum imp-nucleotidase mutant D172N
Analyse Structure of imp bound plasmodium falciparum imp-nucleotidase mutant D172N in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RME
- Type
- protein
- Length
- 3,010 residues
- Chains
- 8
- 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
- IMP, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 6 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 | 373 | 48% helix, 14% strand | A0A144A134 |
| B, D | Imp-specific 5'-nucleotidase, putative (EC 3.1.3.5) | protein | 375 | 47% helix, 15% strand | A0A144A134 |
| C | Imp-specific 5'-nucleotidase, putative (EC 3.1.3.5) | protein | 385 | 49% helix, 14% strand | A0A144A134 |
| E, H | Imp-specific 5'-nucleotidase, putative (EC 3.1.3.5) | protein | 376 | 49% helix, 14% strand | A0A144A134 |
| F | Imp-specific 5'-nucleotidase, putative (EC 3.1.3.5) | protein | 378 | 47% helix, 13% strand | A0A144A134 |
| G | Imp-specific 5'-nucleotidase, putative (EC 3.1.3.5) | protein | 372 | 49% helix, 15% strand | A0A144A134 |
Ligands and binding sites
- IMP · Inosinic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
- GOL · Glycerol · additive · 2 copies · chains D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 841 | 0.81 | 0.84 | 108 | empty |
| 2 | 1026 | 0.80 | 0.82 | 100 | empty |
| 3 | 464 | 0.79 | 0.86 | 68 | empty |
| 4 | 150 | 0.77 | 0.94 | 29 | empty |
| 5 | 318 | 0.77 | 0.88 | 56 | empty |
Interfaces
15 interfaces between chains.
- A–B · 1198 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1197 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 1185 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 1170 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1094 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 6RME · Structure of IMP bound Plasmodium falciparum IMP-nucleotidase mutant D172N · 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 6RME · PDBe 6RME · UniProt A0A144A134
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