Research workbench
Crystal structure of a protein of unknown function MM2497 from methanosarcina mazei GO1, probable nucleotidyltransferase
Analyse Crystal structure of a protein of unknown function MM2497 from methanosarcina… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2I5E
- Type
- protein
- Length
- 420 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hypothetical protein MM_2497
- UniProt
- Q8PU52
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Hypothetical protein MM_2497 | protein | 210 | 36% helix, 20% strand | Q8PU52 |
Ligands and binding sites
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 5 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.79 | 0.97 | 17 | TRS |
| 2 | 550 | 0.75 | 0.82 | 46 | TRS |
| 3 | 523 | 0.74 | 0.82 | 49 | TRS, PEG |
| 4 | 60 | 0.27 | 0.73 | 20 | empty |
| 5 | 55 | 0.24 | 0.72 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1193 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 2I5E · Crystal Structure of a Protein of Unknown Function MM2497 from Methanosarcina mazei Go1… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8PU52 · AlphaFold monomer V2.0 prediction for 2-phospho-L-lactate guanylyltransferase (Q8PU52) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 Q8PU52
- Elsewhere: RCSB PDB 2I5E · PDBe 2I5E · UniProt Q8PU52
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.