Research workbench
Crystal structure of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase from klebsiella aerogenes (P1 form)
Analyse Crystal structure of 2,3-diketo-5-methylthiopentyl-1-phosphate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8DOP
- Type
- protein
- Length
- 1,753 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2,3-diketo-5-methylthiopentyl-1-phosphate enolase- phosphatase
- EC
- 4.1.1.23
- UniProt
- A0A0M3H420
- Ligands
- NA, IOD
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 8 distinct chains · 50% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 2,3-diketo-5-methylthiopentyl-1-phosphate enolase- phosphatase (EC 4.1.1.23) | protein | 216 | 50% helix, 18% strand | A0A0M3H420 |
| B | 2,3-diketo-5-methylthiopentyl-1-phosphate enolase- phosphatase (EC 4.1.1.23) | protein | 214 | 50% helix, 18% strand | A0A0M3H420 |
| C | 2,3-diketo-5-methylthiopentyl-1-phosphate enolase- phosphatase (EC 4.1.1.23) | protein | 215 | 52% helix, 18% strand | A0A0M3H420 |
| D | 2,3-diketo-5-methylthiopentyl-1-phosphate enolase- phosphatase (EC 4.1.1.23) | protein | 215 | 52% helix, 18% strand | A0A0M3H420 |
| E | 2,3-diketo-5-methylthiopentyl-1-phosphate enolase- phosphatase (EC 4.1.1.23) | protein | 221 | 48% helix, 19% strand | A0A0M3H420 |
| F | 2,3-diketo-5-methylthiopentyl-1-phosphate enolase- phosphatase (EC 4.1.1.23) | protein | 227 | 50% helix, 17% strand | A0A0M3H420 |
| G | 2,3-diketo-5-methylthiopentyl-1-phosphate enolase- phosphatase (EC 4.1.1.23) | protein | 224 | 50% helix, 17% strand | A0A0M3H420 |
| H | 2,3-diketo-5-methylthiopentyl-1-phosphate enolase- phosphatase (EC 4.1.1.23) | protein | 221 | 49% helix, 18% strand | A0A0M3H420 |
Ligands and binding sites
- NA · Sodium ion · metal · 6 copies · chains A, B, C, D, E, H
- IOD · Iodide ion · ion · 12 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.81 | 0.98 | 25 | empty |
| 2 | 124 | 0.80 | 0.98 | 26 | empty |
| 3 | 124 | 0.80 | 0.97 | 27 | empty |
| 4 | 112 | 0.78 | 0.97 | 27 | empty |
| 5 | 965 | 0.77 | 0.79 | 92 | IOD, NA |
Interfaces
12 interfaces between chains.
- C–D · 1877 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1842 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1811 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 1735 Ų buried · 13 hydrogen bonds · protein-protein
- D–G · 455 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 8DOP · Crystal structure of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase-phosphatase from… · 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 A0A0M3H420
- Elsewhere: RCSB PDB 8DOP · PDBe 8DOP · UniProt A0A0M3H420
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