Research workbench
Crystal structure of E72A mutant of ancestral protein ancmt of ADP- dependent sugar kinases family
Analyse Crystal structure of E72A mutant of ancestral protein ancmt of ADP- dependent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KKG
- Type
- protein
- Length
- 902 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ancmt E72A
- Ligands
- AMP, IOD
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ancmt E72A | protein | 449 | 45% helix, 20% strand | — |
| B | Ancmt E72A | protein | 453 | 43% helix, 21% strand | — |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · chains A
- IOD · Iodide ion · ion · 12 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1200 | 0.82 | 0.83 | 116 | IOD, GOL |
| 2 | 1109 | 0.78 | 0.80 | 118 | AMP, IOD |
| 3 | 106 | 0.46 | 0.79 | 15 | IOD |
| 4 | 98 | 0.43 | 0.78 | 23 | empty |
| 5 | 72 | 0.38 | 0.78 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 628 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5KKG · Crystal structure of E72A mutant of ancestral protein ancMT of ADP-dependent sugar… · 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
- Elsewhere: RCSB PDB 5KKG · PDBe 5KKG
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