MolNFT v1 · #158544 · protein

ECAII(D90T,K162T) mutant in complex with citrate at pH 7

6NX9 · L-asparaginase 2: “ECAII(D90T,K162T) mutant in complex with citrate at pH 7”. X-ray diffraction, 10 pockets (best druggability 0.66). MolNFT v1 #158544 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6NX9
Type: protein
Length: 1,256 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-asparaginase 2
EC: 3.5.1.1
UniProt: P00805
Pockets: 10 · best druggability 0.66

Structure

x-ray diffraction · 3 distinct chains · 34% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	L-asparaginase 2 (EC 3.5.1.1)	protein	319	34% helix, 22% strand	P00805
B	L-asparaginase 2 (EC 3.5.1.1)	protein	311	35% helix, 22% strand	P00805
C, D	L-asparaginase 2 (EC 3.5.1.1)	protein	313	34% helix, 22% strand	P00805

Ligands and binding sites

ACY · Acetic acid · additive · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 3 copies · chains C, D
IMD · Imidazole · additive · chains A

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

Pockets

10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	140	0.66	0.88	31	empty
2	140	0.65	0.87	29	empty
3	237	0.54	0.77	33	ACY
4	225	0.53	0.77	32	GOL, ACY
5	219	0.51	0.76	31	ACY

Interfaces

3 interfaces between chains.

A–B · 2052 Å² buried · 37 hydrogen bonds · protein-protein
C–D · 2041 Å² buried · 38 hydrogen bonds · protein-protein
A–C · 153 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6NX9 · ECAII(D90T,K162T) mutant in complex with citrate at pH 7 · the same entry in another collection · chain D against D, TM-score 1.00
P00805 · AlphaFold monomer V2.0 prediction for L-asparaginase 2 (P00805) · a predicted model of the same protein · chain B against A, TM-score 0.99

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 P00805
Elsewhere: RCSB PDB 6NX9 · PDBe 6NX9 · UniProt P00805

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