MolNFT v1 · #4525 · protein
Crystal structure of giardia guanine phosphoribosyltransferase complexed with a transition state analogue
1DQN: “Crystal structure of giardia guanine phosphoribosyltransferase complexed with a transition state analogue”. X-ray diffraction, 3 ligands (IMU, POP, MG), 9 pockets (best druggability 0.61). MolNFT v1 #4525 on GenesisL1: 3D structure…
- PDB
- 1DQN
- Type
- protein
- Length
- 460 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine phosphoribosyltransferase
- EC
- 2.4.2.8
- UniProt
- Q24973
- Ligands
- IMU, POP, MG
- Pockets
- 9 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Guanine phosphoribosyltransferase (EC 2.4.2.8) | protein | 230 | 35% helix, 24% strand | Q24973 |
Ligands and binding sites
- IMU · Phosphoric acid mono-[5-(2-amino-4-oxo-4,5-dihydro-3H-pyrrolo[3,2-d]pyrimidin-7-yl)-3,4-dihydroxy-pyrrolidin-2-ylmethyl] ester · ligand · 2 copies · chains A, B
- POP · Pyrophosphate 2- · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A
- IPA · Isopropyl alcohol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 245 | 0.61 | 0.80 | 35 | empty |
| 2 | 265 | 0.56 | 0.77 | 27 | IMU, POP |
| 3 | 276 | 0.55 | 0.76 | 27 | MG, IMU, POP |
| 4 | 130 | 0.42 | 0.76 | 25 | empty |
| 5 | 83 | 0.33 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1782 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 1DQN · Crystal structure of giardia guanine phosphoribosyltransferase complexed with a… · 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 Q24973
- Elsewhere: RCSB PDB 1DQN · PDBe 1DQN · UniProt Q24973
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