Research workbench
M. jannaschii adh synthase covalently bound to dihydroxyacetone phosphate
Analyse M. jannaschii adh synthase covalently bound to dihydroxyacetone phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QJH
- Type
- protein
- Length
- 5,286 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative aldolase MJ0400
- EC
- 4.2.1.-
- UniProt
- Q57843
- Ligands
- 13P
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F, G, H, I, J, K, M, N, O, P, Q, S, T | Putative aldolase MJ0400 (EC 4.2.1.-) | protein | 264 | 42% helix, 17% strand | Q57843 |
| C | Putative aldolase MJ0400 (EC 4.2.1.-) | protein | 265 | 42% helix, 17% strand | Q57843 |
| D, R | Putative aldolase MJ0400 (EC 4.2.1.-) | protein | 266 | 42% helix, 17% strand | Q57843 |
| L | Putative aldolase MJ0400 (EC 4.2.1.-) | protein | 265 | 41% helix, 17% strand | Q57843 |
Ligands and binding sites
- 13P · 1,3-dihydroxyacetonephosphate · ligand · 20 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T
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 | 1026 | 0.77 | 0.79 | 133 | empty |
| 2 | 1051 | 0.77 | 0.79 | 131 | empty |
| 3 | 1127 | 0.75 | 0.78 | 102 | 13P |
| 4 | 1092 | 0.75 | 0.78 | 126 | empty |
| 5 | 1056 | 0.75 | 0.78 | 120 | empty |
Interfaces
52 interfaces between chains.
- D–E · 1357 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1352 Ų buried · 16 hydrogen bonds · protein-protein
- P–T · 1350 Ų buried · 17 hydrogen bonds · protein-protein
- F–J · 1349 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 1346 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 covalent (covalent ligand).
Compared structures
- 2QJH · M. jannaschii ADH synthase covalently bound to dihydroxyacetone phosphate · the same entry in another collection · chain K against K, 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 Q57843
- Elsewhere: RCSB PDB 2QJH · PDBe 2QJH · UniProt Q57843
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.