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Crystal structure of bstmcal bound with ampcpp

Analyse Crystal structure of bstmcal bound with ampcpp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5Y0Q
Type: protein
Length: 802 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: UPF0348 protein B4417_3650
UniProt: A0A164SIT4
Ligands: APC
Pockets: 9 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 54% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	UPF0348 protein B4417_3650	protein	401	54% helix, 12% strand	A0A164SIT4

Ligands and binding sites

APC · Diphosphomethylphosphonic acid adenosyl ester · ligand · 2 copies · chains A, 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	314	0.74	0.86	36	APC
2	380	0.72	0.84	45	APC
3	638	0.69	0.78	74	empty
4	56	0.40	0.81	13	empty
5	154	0.39	0.73	25	empty

Interfaces

1 interface between chains.

A–B · 1140 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

5Y0Q · Crystal structure of BsTmcAL bound with AMPCPP · 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 A0A164SIT4
Elsewhere: RCSB PDB 5Y0Q · PDBe 5Y0Q · UniProt A0A164SIT4

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