MolNFT v1 · #49197 · protein
Crystal structure of TM_1862 from thermotoga maritima. northeast structural genomics consortium target VR77
2QGQ · Protein TM_1862: “Crystal structure of TM_1862 from thermotoga maritima. northeast structural genomics consortium target VR77”. X-ray diffraction, 20 pockets (best druggability 0.75). MolNFT v1 #49197 on GenesisL1: 3D structure…
- PDB
- 2QGQ
- Type
- protein
- Length
- 2,158 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein TM_1862
- UniProt
- Q9X2H6
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein TM_1862 | protein | 272 | 36% helix, 26% strand | Q9X2H6 |
| B, E, H | Protein TM_1862 | protein | 270 | 37% helix, 27% strand | Q9X2H6 |
| C, D, F, G | Protein TM_1862 | protein | 269 | 36% helix, 27% strand | Q9X2H6 |
Ligands and binding sites
- CXS · 3-cyclohexyl-1-propylsulfonic acid · additive · 4 copies · chains A, B, D, E, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 813 | 0.75 | 0.79 | 62 | empty |
| 2 | 1045 | 0.74 | 0.77 | 75 | empty |
| 3 | 722 | 0.74 | 0.79 | 62 | empty |
| 4 | 1161 | 0.73 | 0.76 | 83 | empty |
| 5 | 667 | 0.72 | 0.79 | 54 | empty |
Interfaces
14 interfaces between chains.
- E–F · 621 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 609 Ų buried · 3 hydrogen bonds · protein-protein
- C–G · 600 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 599 Ų buried · 11 hydrogen bonds · protein-protein
- D–H · 596 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified (engineered).
Compared structures
- 2QGQ · Crystal structure of TM_1862 from Thermotoga maritima. Northeast Structural Genomics… · the same entry in another collection · chain H against H, TM-score 1.00
- Q9X2H6 · AlphaFold monomer V2.0 prediction for ribosomal protein S12 methylthiotransferase rimo… · a predicted model of the same protein · chain C 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 Q9X2H6
- Elsewhere: RCSB PDB 2QGQ · PDBe 2QGQ · UniProt Q9X2H6
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