Research workbench
M. jannaschii adh synthase complexed with dihydroxyacetone phosphate and glycerol
Analyse M. jannaschii adh synthase complexed with dihydroxyacetone phosphate and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QJI
- Type
- protein
- Length
- 5,418 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 0.82
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S | Putative aldolase MJ0400 (EC 4.2.1.-) | protein | 271 | 39% helix, 16% strand | Q57843 |
| T | Putative aldolase MJ0400 (EC 4.2.1.-) | protein | 269 | 39% helix, 16% 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
- GOL · Glycerol · additive · 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 | 428 | 0.82 | 0.90 | 65 | empty |
| 2 | 556 | 0.80 | 0.87 | 69 | empty |
| 3 | 164 | 0.80 | 0.96 | 34 | empty |
| 4 | 557 | 0.80 | 0.86 | 60 | empty |
| 5 | 876 | 0.79 | 0.82 | 88 | empty |
Interfaces
52 interfaces between chains.
- F–G · 1443 Ų buried · 17 hydrogen bonds · protein-protein
- H–I · 1431 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 1415 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 1409 Ų buried · 14 hydrogen bonds · protein-protein
- G–H · 1408 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 covalent (covalent ligand).
Compared structures
- 2QJI · M. jannaschii ADH synthase complexed with dihydroxyacetone phosphate and glycerol · the same entry in another collection · chain I against I, 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 2QJI · PDBe 2QJI · UniProt Q57843
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