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Structure and function of ybdk

Analyse Structure and function of ybdk in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1R8G
Type: protein
Length: 710 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical protein ybdk
EC: 6.3.-.-
UniProt: P77213
Pockets: 10 · best druggability 0.79

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hypothetical protein ybdk (EC 6.3.-.-)	protein	352	45% helix, 17% strand	P77213
B	Hypothetical protein ybdk (EC 6.3.-.-)	protein	358	47% helix, 17% strand	P77213

Pockets

10 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	534	0.79	0.85	47	empty
2	131	0.77	0.95	31	empty
3	763	0.72	0.78	73	empty
4	387	0.68	0.80	33	empty
5	490	0.66	0.78	56	empty

Interfaces

1 interface between chains.

A–B · 1820 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 20 modified (engineered).

Compared structures

1R8G · Structure and function of YbdK · the same entry in another collection · chain A against A, TM-score 1.00
P77213 · AlphaFold monomer V2.0 prediction for putative glutamate--cysteine ligase 2 (P77213) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P77213
Elsewhere: RCSB PDB 1R8G · PDBe 1R8G · UniProt P77213

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