Research workbench

Crystal structure of hygx from streptomyces hygroscopicus with nickel and 2-oxoglutarate bound

Analyse Crystal structure of hygx from streptomyces hygroscopicus with nickel and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4XCA
Type: protein
Length: 1,005 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: OXIDASE/HYDROXYLASE
UniProt: Q2MFS1
Ligands: AKG, NI, CS
Pockets: 14 · best druggability 0.86

Structure

x-ray diffraction · 4 distinct chains · 25% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	OXIDASE/HYDROXYLASE	protein	256	27% helix, 27% strand	Q2MFS1
B	OXIDASE/HYDROXYLASE	protein	242	24% helix, 29% strand	Q2MFS1
C	OXIDASE/HYDROXYLASE	protein	253	25% helix, 28% strand	Q2MFS1
D	OXIDASE/HYDROXYLASE	protein	254	23% helix, 28% strand	Q2MFS1

Ligands and binding sites

AKG · 2-oxoglutaric acid · ligand · 4 copies · chains A, B, C, D
NI · Nickel (II) ion · metal · 4 copies · chains A, B, C, D
CS · Cesium ion · metal · 3 copies · chains B, C, D
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A

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

Pockets

14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1090	0.86	0.86	76	empty
2	399	0.78	0.87	42	NI, AKG
3	409	0.75	0.85	44	NI, AKG
4	363	0.74	0.85	39	NI, AKG
5	357	0.73	0.84	43	NI, AKG

Interfaces

6 interfaces between chains.

B–C · 2099 Å² buried · 33 hydrogen bonds · protein-protein
A–D · 2093 Å² buried · 34 hydrogen bonds · protein-protein
A–C · 1324 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 1247 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 142 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4XCA · Crystal Structure of HygX from Streptomyces hygroscopicus with nickel and 2-oxoglutarate… · 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 Q2MFS1
Elsewhere: RCSB PDB 4XCA · PDBe 4XCA · UniProt Q2MFS1

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.