Research workbench
Dhodb-I74D mutant
Analyse Dhodb-I74D mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KSW
- Type
- protein
- Length
- 1,135 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dihydroorotate dehydrogenase; Dihydroorotate dehydrogenase B (NAD(+)), electron transfer…
- EC
- 1.3.1.14
- UniProt
- A0A089ZD72, A0A0V8EGX5
- Ligands
- FMN, FAD, FES, CL
- Pockets
- 14 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dihydroorotate dehydrogenase (EC 1.3.1.14) | protein | 306 | 35% helix, 20% strand | A0A089ZD72 |
| B, D | Dihydroorotate dehydrogenase B (NAD(+)), electron transfer subunit | protein | 262 | 20% helix, 34% strand | A0A0V8EGX5 |
| C | Dihydroorotate dehydrogenase (EC 1.3.1.14) | protein | 305 | 35% helix, 20% strand | A0A089ZD72 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B, D, C
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B, D, C
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains B, D
- CL · Chloride ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 291 | 0.77 | 0.89 | 62 | FMN |
| 2 | 464 | 0.76 | 0.85 | 58 | FMN, CL |
| 3 | 485 | 0.69 | 0.79 | 40 | FAD |
| 4 | 468 | 0.68 | 0.79 | 40 | FAD |
| 5 | 632 | 0.66 | 0.76 | 51 | empty |
Interfaces
5 interfaces between chains.
- D–C · 1408 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1302 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 414 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 286 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 49 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5KSW · DHODB-I74D mutant · the same entry in another collection · chain A 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 A0A089ZD72
- Every structure of UniProt A0A0V8EGX5
- Elsewhere: RCSB PDB 5KSW · PDBe 5KSW · UniProt A0A089ZD72 · UniProt A0A0V8EGX5
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