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Crystal structure of 4-oxalocrotonate tautomerase after incubation with 5-fluoro-2-hydroxy-2,4-pentadienoate
Analyse Crystal structure of 4-oxalocrotonate tautomerase after incubation with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BGN
- Type
- protein
- Length
- 888 residues
- Chains
- 15
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-hydroxymuconate tautomerase
- EC
- 5.3.2.6
- UniProt
- Q01468
- Ligands
- 6Y5, NO3
- Pockets
- 17 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, F, H, N, O | 2-hydroxymuconate tautomerase (EC 5.3.2.6) | protein | 59 | 42% helix, 31% strand | Q01468 |
| B, D, G, J, K, L | 2-hydroxymuconate tautomerase (EC 5.3.2.6) | protein | 60 | 42% helix, 30% strand | Q01468 |
| E, I, M | 2-hydroxymuconate tautomerase (EC 5.3.2.6) | protein | 58 | 43% helix, 33% strand | Q01468 |
Ligands and binding sites
- 6Y5 · 5-fluoranyl-2-oxidanylidene-pentanoic acid · ligand · 15 copies · chains A, B, C, D, E, I, H, F, G, J, K, O, N, L, M
- NO3 · Nitrate ion · ion · 3 copies · chains G, H, J, K
- GOL · Glycerol · additive · 18 copies · chains B, D, H, E, F, I, G, J, N, K, O, L, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 143 | 0.77 | 0.94 | 30 | empty |
| 2 | 343 | 0.73 | 0.85 | 50 | GOL |
| 3 | 885 | 0.70 | 0.76 | 83 | GOL |
| 4 | 355 | 0.60 | 0.77 | 40 | NO3, 6Y5 |
| 5 | 189 | 0.52 | 0.78 | 27 | GOL |
Interfaces
32 interfaces between chains.
- M–N · 925 Ų buried · 15 hydrogen bonds · protein-protein
- J–K · 915 Ų buried · 15 hydrogen bonds · protein-protein
- G–H · 913 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 901 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 897 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 covalent (covalent ligand).
Compared structures
- 6BGN · Crystal Structure of 4-Oxalocrotonate Tautomerase After Incubation with… · 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 Q01468
- Elsewhere: RCSB PDB 6BGN · PDBe 6BGN · UniProt Q01468
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