MolNFT v1 · #124007 · protein
Crystal structure of ancestral protein ancmt of ADP-dependent sugar kinases family.
5K27: “Crystal structure of ancestral protein ancmt of ADP-dependent sugar kinases family.”. X-ray diffraction, 2 ligands (AMP, IOD), 7 pockets (best druggability 0.79). MolNFT v1 #124007 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5K27
- Type
- protein
- Length
- 902 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ancmt
- EC
- 2.7.1.146, 2.7.1.147
- Ligands
- AMP, IOD
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ancmt (EC 2.7.1.146, 2.7.1.147) | protein | 453 | 46% helix, 20% strand | — |
| B | Ancmt (EC 2.7.1.146, 2.7.1.147) | protein | 449 | 45% helix, 20% strand | — |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- IOD · Iodide ion · ion · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 860 | 0.79 | 0.82 | 93 | AMP, IOD |
| 2 | 1094 | 0.79 | 0.81 | 125 | AMP, IOD |
| 3 | 515 | 0.70 | 0.80 | 48 | empty |
| 4 | 122 | 0.42 | 0.76 | 21 | empty |
| 5 | 54 | 0.36 | 0.79 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 537 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5K27 · Crystal structure of ancestral protein ancMT of ADP-dependent sugar kinases family. · 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 5K27 · PDBe 5K27
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