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Crystal structure of apo hygx from streptomyces hygroscopicus

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

PDB: 4XC9
Type: protein
Length: 1,477 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: OXIDASE/HYDROXYLASE
UniProt: Q2MFS1
Pockets: 19 · best druggability 0.86

Structure

x-ray diffraction · 5 distinct chains · 24% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	OXIDASE/HYDROXYLASE	protein	247	25% helix, 28% strand	Q2MFS1
B	OXIDASE/HYDROXYLASE	protein	248	23% helix, 27% strand	Q2MFS1
C, E	OXIDASE/HYDROXYLASE	protein	246	25% helix, 28% strand	Q2MFS1
D	OXIDASE/HYDROXYLASE	protein	247	24% helix, 29% strand	Q2MFS1
F	OXIDASE/HYDROXYLASE	protein	243	25% helix, 26% strand	Q2MFS1

Ligands and binding sites

TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 6 copies · chains A, B, C, D, E, F

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

Pockets

19 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	1092	0.86	0.87	76	empty
2	405	0.76	0.85	52	empty
3	401	0.75	0.85	49	empty
4	398	0.74	0.85	44	empty
5	454	0.74	0.84	53	empty

Interfaces

8 interfaces between chains.

B–C · 2140 Å² buried · 36 hydrogen bonds · protein-protein
A–D · 2116 Å² buried · 34 hydrogen bonds · protein-protein
E–F · 2114 Å² buried · 31 hydrogen bonds · protein-protein
A–C · 1343 Å² buried · 8 hydrogen bonds · protein-protein
B–D · 1319 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

4XC9 · Crystal Structure of apo HygX from Streptomyces hygroscopicus · 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 4XC9 · PDBe 4XC9 · UniProt Q2MFS1

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