MolNFT v1 · #101637 · protein

Crystal structure of abp-D197A, a catalytic mutant of a GH27-B-L- arabinopyranosidase from geobacillus stearothermophilus

4NXK · Abp, a GH27 beta-L-arabinopyranosidase: “Crystal structure of abp-D197A, a catalytic mutant of a GH27-B-L- arabinopyranosidase from geobacillus…”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.75). MolNFT v1…

PDB: 4NXK
Type: protein
Length: 3,447 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Abp, a GH27 beta-L-arabinopyranosidase
Ligands: SO4
Pockets: 20 · best druggability 0.75

Structure

x-ray diffraction · 3 distinct chains · 33% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, E	Abp, a GH27 beta-L-arabinopyranosidase	protein	431	33% helix, 25% strand	—
B, C, F, G, H	Abp, a GH27 beta-L-arabinopyranosidase	protein	430	33% helix, 25% strand	—
D	Abp, a GH27 beta-L-arabinopyranosidase	protein	435	33% helix, 24% strand	—

Ligands and binding sites

SO4 · Sulfate ion · ion · 66 copies · chains A, E, B, C, D, G, H, F
GOL · Glycerol · additive · 30 copies · chains A, E, B, C, H, D, G, F
CIT · Citric acid · additive · 6 copies · chains A, B, C, D, E, G

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

Pockets

20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	972	0.75	0.78	92	SO4, GOL
2	1196	0.72	0.76	98	SO4
3	569	0.61	0.74	70	SO4
4	423	0.61	0.76	35	empty
5	383	0.59	0.76	33	SO4

Interfaces

13 interfaces between chains.

G–H · 835 Å² buried · 14 hydrogen bonds · protein-protein
C–D · 827 Å² buried · 10 hydrogen bonds · protein-protein
F–H · 825 Å² buried · 7 hydrogen bonds · protein-protein
A–B · 823 Å² buried · 10 hydrogen bonds · protein-protein
E–F · 817 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

4NXK · Crystal structure of Abp-D197A, a catalytic mutant of a GH27-b-L-arabinopyranosidase from… · 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
Elsewhere: RCSB PDB 4NXK · PDBe 4NXK

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