MolNFT v1 · #109761 · protein

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

4XCB · OXIDASE/HYDROXYLASE: “Crystal structure of hygx from streptomyces hygroscopicus with nickel, 2-oxoglutarate, and hygromycin B bound”. X-ray diffraction, 3 ligands (AKG, HY0, NI), 13 pockets (best druggability 0.85). MolNFT v1…

PDB: 4XCB
Type: protein
Length: 1,024 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: OXIDASE/HYDROXYLASE
UniProt: Q2MFS1
Ligands: AKG, HY0, NI
Pockets: 13 · best druggability 0.85

Structure

x-ray diffraction · 4 distinct chains · 23% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	OXIDASE/HYDROXYLASE	protein	260	24% helix, 27% strand	Q2MFS1
B	OXIDASE/HYDROXYLASE	protein	259	23% helix, 28% strand	Q2MFS1
C	OXIDASE/HYDROXYLASE	protein	254	24% helix, 28% strand	Q2MFS1
D	OXIDASE/HYDROXYLASE	protein	251	21% helix, 29% strand	Q2MFS1

Ligands and binding sites

AKG · 2-oxoglutaric acid · ligand · 4 copies · chains A, B, C, D
HY0 · Hygromycin B variant · ligand · 4 copies · chains A, B, C, D
NI · Nickel (II) ion · metal · 4 copies · chains A, B, C, D

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

Pockets

13 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	1089	0.85	0.86	75	empty
2	475	0.78	0.85	45	NI, AKG, HY0
3	443	0.78	0.86	49	NI, AKG, HY0
4	493	0.77	0.85	54	NI, AKG, HY0
5	428	0.76	0.85	50	NI, AKG, HY0

Interfaces

6 interfaces between chains.

C–D · 2104 Å² buried · 42 hydrogen bonds · protein-protein
A–B · 2086 Å² buried · 43 hydrogen bonds · protein-protein
A–C · 1350 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 1345 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 138 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

4XCB · Crystal Structure of HygX from Streptomyces hygroscopicus with nickel, 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 4XCB · PDBe 4XCB · UniProt Q2MFS1

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