MolNFT v1 · #128887 · protein
Crystal structure of sorbitol-6-phosphate 2-dehydrogenase srld from erwinia amylovora
5O3Z · Sorbitol-6-phosphate dehydrogenase: “Crystal structure of sorbitol-6-phosphate 2-dehydrogenase srld from erwinia amylovora”. X-ray diffraction, 1 ligand (CL), 20 pockets (best druggability 0.87). MolNFT v1 #128887 on GenesisL1: 3D…
- PDB
- 5O3Z
- Type
- protein
- Length
- 3,095 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sorbitol-6-phosphate dehydrogenase
- EC
- 1.1.1.140
- UniProt
- D4I194
- Ligands
- CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, G, H, I, K | Sorbitol-6-phosphate dehydrogenase (EC 1.1.1.140) | protein | 258 | 53% helix, 15% strand | D4I194 |
| B | Sorbitol-6-phosphate dehydrogenase (EC 1.1.1.140) | protein | 257 | 53% helix, 15% strand | D4I194 |
| F, J | Sorbitol-6-phosphate dehydrogenase (EC 1.1.1.140) | protein | 259 | 53% helix, 15% strand | D4I194 |
| L | Sorbitol-6-phosphate dehydrogenase (EC 1.1.1.140) | protein | 256 | 53% helix, 14% strand | D4I194 |
Ligands and binding sites
- CL · Chloride ion · ion · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 927 | 0.87 | 0.88 | 94 | empty |
| 2 | 428 | 0.86 | 0.94 | 50 | empty |
| 3 | 929 | 0.86 | 0.87 | 96 | empty |
| 4 | 418 | 0.86 | 0.93 | 48 | empty |
| 5 | 433 | 0.85 | 0.93 | 52 | empty |
Interfaces
26 interfaces between chains.
- A–C · 1666 Ų buried · 16 hydrogen bonds · protein-protein
- J–L · 1656 Ų buried · 14 hydrogen bonds · protein-protein
- I–K · 1651 Ų buried · 13 hydrogen bonds · protein-protein
- F–H · 1650 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 1643 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5O3Z · Crystal structure of Sorbitol-6-Phosphate 2-dehydrogenase SrlD from Erwinia amylovora · 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 D4I194
- Elsewhere: RCSB PDB 5O3Z · PDBe 5O3Z · UniProt D4I194
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