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Crystal structure of L,D-transpeptidase (yku) from stackebrandtia nassauensis

Analyse Crystal structure of L,D-transpeptidase (yku) from stackebrandtia nassauensis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5BMQ
Type: protein
Length: 205 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: ERFK/YBIS/YCFS/YNHG family protein
EC: 3.-.-.-
UniProt: D3Q1D9
Ligands: SO4
Pockets: 3 · best druggability 0.48

Structure

x-ray diffraction · 1 distinct chain · 25% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	ERFK/YBIS/YCFS/YNHG family protein (EC 3.-.-.-)	protein	205	25% helix, 27% strand	D3Q1D9

Ligands and binding sites

SO4 · Sulfate ion · ion · 2 copies · chains A
DIO · 1,4-diethylene dioxide · additive · chains A
GOL · Glycerol · additive · chains A

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	117	0.48	0.80	22	empty
2	84	0.40	0.78	15	empty
3	61	0.31	0.75	14	empty

Modifications

Observed in the structure: 3 modified, 2 disulfide (engineered, disulfide).

Compared structures

5BMQ · Crystal structure of L,D-transpeptidase (Yku) from Stackebrandtia nassauensis · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt D3Q1D9
Elsewhere: RCSB PDB 5BMQ · PDBe 5BMQ · UniProt D3Q1D9

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