MolNFT v1 · #124619 · protein

Crystal structure of E72A mutant of ancestral protein ancmt of ADP- dependent sugar kinases family

5KKG · Ancmt E72A: “Crystal structure of E72A mutant of ancestral protein ancmt of ADP- dependent sugar kinases family”. X-ray diffraction, 2 ligands (AMP, IOD), 9 pockets (best druggability 0.82). MolNFT v1 #124619 on GenesisL1: 3D…

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.

Pocket	Volume (Å³)	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 Å² 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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