MolNFT v1 · #127625 · protein

Structure of XECO2 acetyltransferase domain bound to K106-CoA conjugate

5N22: “Structure of XECO2 acetyltransferase domain bound to K106-CoA conjugate”. X-ray diffraction, 1 ligand (8HB), 13 pockets (best druggability 0.76). MolNFT v1 #127625 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5N22
Type: protein
Length: 691 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: XECO2; Gly-ala-lys-lyx-asp-gln-tyr-phe-leu
UniProt: A8QZK6
Ligands: 8HB
Pockets: 13 · best druggability 0.76

Structure

x-ray diffraction · 6 distinct chains · 27% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	XECO2	protein	168	26% helix, 32% strand	A8QZK6
B	XECO2	protein	168	28% helix, 32% strand	A8QZK6
C	XECO2	protein	168	26% helix, 32% strand	A8QZK6
D	XECO2	protein	167	28% helix, 32% strand	A8QZK6
E, G	Gly-ala-lys-lyx-asp-gln-tyr-phe-leu	protein	9	0% helix, 33% strand	—
J, L	Gly-ala-lys-lyx-asp-gln-tyr-phe-leu	protein	1	0% helix, 0% strand	—

Ligands and binding sites

8HB · (2~{S})-2-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R}, 5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethylsulfanyl]p ropanoic acid · ligand · 4 copies · chains A, B, E, C, G, J, D, L

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	859	0.76	0.79	91	8HB
2	865	0.74	0.78	68	empty
3	570	0.71	0.80	67	8HB
4	114	0.59	0.85	18	empty
5	209	0.59	0.80	31	8HB

Interfaces

11 interfaces between chains.

A–D · 730 Å² buried · 4 hydrogen bonds · protein-protein
A–E · 723 Å² buried · 12 hydrogen bonds · protein-protein
C–G · 715 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 696 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 478 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

5N22 · Structure of xEco2 acetyltransferase domain bound to K106-CoA conjugate · 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 A8QZK6
Elsewhere: RCSB PDB 5N22 · PDBe 5N22 · UniProt A8QZK6

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