MolNFT v1 · #156497 · protein
Crystal structure of mycobacterium smegmatis MUTT1 in complex with gmppnp (GDP)
6M65 · Hydrolase, nudix family protein: “Crystal structure of mycobacterium smegmatis MUTT1 in complex with gmppnp (GDP)”. X-ray diffraction, 3 ligands (GDP, POP, MG), 3 pockets (best druggability 0.45). MolNFT v1 #156497 on GenesisL1: 3D…
- PDB
- 6M65
- Type
- protein
- Length
- 290 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hydrolase, nudix family protein
- UniProt
- A0QUZ2
- Ligands
- GDP, POP, MG
- Pockets
- 3 · best druggability 0.45
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hydrolase, nudix family protein | protein | 290 | 34% helix, 34% strand | A0QUZ2 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · chains A
- POP · Pyrophosphate 2- · ligand · chains A
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 5 copies · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 96 | 0.45 | 0.80 | 25 | empty |
| 2 | 97 | 0.41 | 0.78 | 16 | EDO |
| 3 | 59 | 0.34 | 0.77 | 13 | GDP, MG |
Compared structures
- 6M65 · Crystal structure of Mycobacterium smegmatis MutT1 in complex with GMPPNP (GDP) · the same entry in another collection · chain A against A, TM-score 1.00
- A0QUZ2 · AlphaFold monomer V2.0 prediction for 8-oxo-(D)GTP phosphatase (A0QUZ2) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 A0QUZ2
- Elsewhere: RCSB PDB 6M65 · PDBe 6M65 · UniProt A0QUZ2
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