MolNFT v1 · #97110 · protein
Crystal structure of D-erythrulose 4-phosphate dehydrogenase from brucella melitensis, solved by iodide sad
4K3Z: “Crystal structure of D-erythrulose 4-phosphate dehydrogenase from brucella melitensis, solved by iodide sad”. X-ray diffraction, 7 pockets (best druggability 0.47). MolNFT v1 #97110 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4K3Z
- Type
- protein
- Length
- 616 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- D-erythrulose 4-phosphate dehydrogenase
- EC
- 1.1.1.-
- UniProt
- Q8YCV0
- Pockets
- 7 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | D-erythrulose 4-phosphate dehydrogenase (EC 1.1.1.-) | protein | 310 | 48% helix, 14% strand | Q8YCV0 |
| B | D-erythrulose 4-phosphate dehydrogenase (EC 1.1.1.-) | protein | 306 | 49% helix, 15% strand | Q8YCV0 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 167 | 0.47 | 0.77 | 34 | GOL |
| 2 | 148 | 0.45 | 0.76 | 29 | EDO |
| 3 | 75 | 0.41 | 0.79 | 13 | EDO |
| 4 | 69 | 0.39 | 0.79 | 13 | empty |
| 5 | 105 | 0.39 | 0.76 | 21 | EDO |
Interfaces
1 interface between chains.
- A–B · 646 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4K3Z · Crystal structure of D-erythrulose 4-phosphate dehydrogenase from Brucella melitensis… · 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 Q8YCV0
- Elsewhere: RCSB PDB 4K3Z · PDBe 4K3Z · UniProt Q8YCV0
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