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Besd with FE(II), chloride, and alpha-ketoglutarate

Analyse Besd with FE(II), chloride, and alpha-ketoglutarate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NIE
Type: protein
Length: 976 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Besd, lysine halogenase
UniProt: G8XHD5
Ligands: LYS, AKG, FE2, FE, CL
Pockets: 10 · best druggability 0.82

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	Besd, lysine halogenase	protein	244	32% helix, 28% strand	G8XHD5
C	Besd, lysine halogenase	protein	244	31% helix, 28% strand	G8XHD5

Ligands and binding sites

LYS · Lysine · ligand · 4 copies · chains A, B, C, D
AKG · 2-oxoglutaric acid · ligand · 4 copies · chains A, B, C, D
FE2 · Fe (II) ion · metal · 4 copies · chains A, B, C, D
FE · Fe (III) ion · metal · chains B, D
CL · Chloride ion · ion · 4 copies · chains A, B, C, D

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

Pockets

10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	153	0.82	0.98	35	LYS, FE2, CL, AKG
2	143	0.81	0.98	35	LYS, FE2, CL, AKG
3	136	0.81	0.98	34	LYS, FE2, CL, AKG
4	143	0.81	0.98	35	LYS, FE2, CL, AKG
5	462	0.75	0.84	55	empty

Interfaces

4 interfaces between chains.

B–C · 1078 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 1013 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 735 Å² buried · 14 hydrogen bonds · protein-protein
B–D · 712 Å² buried · 16 hydrogen bonds · protein-protein

Compared structures

6NIE · BesD with Fe(II), chloride, and alpha-ketoglutarate · the same entry in another collection · chain D against D, TM-score 1.00
G8XHD5 · AlphaFold monomer V2.0 prediction for L-lysine 4-chlorinase (G8XHD5) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 G8XHD5
Elsewhere: RCSB PDB 6NIE · PDBe 6NIE · UniProt G8XHD5

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