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Crystal structure of the guinea pig L-asparaginase 1 catalytic domain

Analyse Crystal structure of the guinea pig L-asparaginase 1 catalytic domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4R8K
Type: protein
Length: 2,827 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Uncharacterized protein
EC: 3.5.1.1
UniProt: H0W0T5
Pockets: 20 · best druggability 0.87

Structure

x-ray diffraction · 5 distinct chains · 30% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Uncharacterized protein (EC 3.5.1.1)	protein	355	30% helix, 24% strand	H0W0T5
B	Uncharacterized protein (EC 3.5.1.1)	protein	347	31% helix, 24% strand	H0W0T5
C, D	Uncharacterized protein (EC 3.5.1.1)	protein	355	30% helix, 22% strand	H0W0T5
E	Uncharacterized protein (EC 3.5.1.1)	protein	353	30% helix, 24% strand	H0W0T5
F, G, H	Uncharacterized protein (EC 3.5.1.1)	protein	354	31% helix, 24% strand	H0W0T5

Ligands and binding sites

EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 8 copies · chains A, D, B, C, E, H, F, 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, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	654	0.87	0.92	118	empty
2	420	0.86	0.93	78	empty
3	339	0.85	0.95	65	empty
4	491	0.84	0.90	94	empty
5	147	0.76	0.94	22	empty

Interfaces

11 interfaces between chains.

E–H · 1656 Å² buried · 24 hydrogen bonds · protein-protein
B–C · 1634 Å² buried · 26 hydrogen bonds · protein-protein
F–G · 1618 Å² buried · 22 hydrogen bonds · protein-protein
A–D · 1617 Å² buried · 26 hydrogen bonds · protein-protein
G–H · 1249 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4R8K · Crystal structure of the guinea pig L-asparaginase 1 catalytic domain · the same entry in another collection · chain G against G, 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 H0W0T5
Elsewhere: RCSB PDB 4R8K · PDBe 4R8K · UniProt H0W0T5

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