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Crystal structure of yokd protein from bacillus subtilis

Analyse Crystal structure of yokd protein from bacillus subtilis in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2NYG
Type: protein
Length: 1,567 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Yokd protein
UniProt: O32003
Ligands: COA
Pockets: 16 · best druggability 0.79

Structure

x-ray diffraction · 5 distinct chains · 37% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Yokd protein	protein	270	38% helix, 20% strand	O32003
B	Yokd protein	protein	251	35% helix, 21% strand	O32003
D	Yokd protein	protein	268	35% helix, 22% strand	O32003
E	Yokd protein	protein	260	39% helix, 21% strand	O32003
F	Yokd protein	protein	248	38% helix, 21% strand	O32003

Ligands and binding sites

COA · Coenzyme A · ligand · 5 copies · chains A, B, C, D, E

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

Pockets

16 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	930	0.79	0.81	101	empty
2	687	0.77	0.82	73	empty
3	893	0.74	0.77	93	empty
4	968	0.70	0.75	92	empty
5	718	0.64	0.74	60	empty

Interfaces

6 interfaces between chains.

C–D · 1428 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 1314 Å² buried · 11 hydrogen bonds · protein-protein
E–F · 947 Å² buried · 10 hydrogen bonds · protein-protein
A–F · 195 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 119 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

2NYG · Crystal structure of YokD protein from Bacillus subtilis · the same entry in another collection · chain F against F, TM-score 1.00
O32003 · AlphaFold monomer V2.0 prediction for spbeta prophage-derived aminoglycoside… · a predicted model of the same protein · chain B 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 O32003
Elsewhere: RCSB PDB 2NYG · PDBe 2NYG · UniProt O32003

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