MolNFT v1 · #121471 · protein
Crystal structure of keto-deoxy-D-galactarate dehydratase complexed with 2-oxoadipic acid
5HWM · Probable 5-dehydro-4-deoxyglucarate dehydratase: “Crystal structure of keto-deoxy-D-galactarate dehydratase complexed with 2-oxoadipic acid”. X-ray diffraction, 1 ligand (OOG), 11 pockets (best druggability 0.65). MolNFT v1 #121471…
- PDB
- 5HWM
- Type
- protein
- Length
- 1,211 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable 5-dehydro-4-deoxyglucarate dehydratase
- EC
- 4.2.1.41
- UniProt
- Q8UB77
- Ligands
- OOG
- Pockets
- 11 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 52% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) | protein | 304 | 52% helix, 13% strand | Q8UB77 |
| B, D | Probable 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) | protein | 303 | 52% helix, 13% strand | Q8UB77 |
| C | Probable 5-dehydro-4-deoxyglucarate dehydratase (EC 4.2.1.41) | protein | 301 | 52% helix, 13% strand | Q8UB77 |
Ligands and binding sites
- OOG · 2-oxoadipic acid · ligand · 4 copies · chains A, B, C, D
- FMT · Formic acid · additive · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.65 | 0.80 | 46 | OOG |
| 2 | 288 | 0.64 | 0.81 | 41 | OOG |
| 3 | 258 | 0.63 | 0.81 | 34 | OOG, FMT |
| 4 | 286 | 0.61 | 0.79 | 38 | OOG, FMT |
| 5 | 80 | 0.38 | 0.77 | 19 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1679 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 1647 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 859 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 854 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 5HWM · Crystal structure of keto-deoxy-D-galactarate dehydratase complexed with 2-oxoadipic acid · the same entry in another collection · chain A against A, TM-score 1.00
- Q8UB77 · AlphaFold monomer V2.0 prediction for probable 5-dehydro-4-deoxyglucarate dehydratase… · a predicted model of the same protein · chain C against A, 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 Q8UB77
- Elsewhere: RCSB PDB 5HWM · PDBe 5HWM · UniProt Q8UB77
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