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ECAI(T162A) mutant in complex with citrate at pH 4

Analyse ECAI(T162A) mutant in complex with citrate at pH 4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NXC
Type: protein
Length: 1,319 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-asparaginase 1
EC: 3.5.1.1
UniProt: P0A962
Ligands: ASN, CL
Pockets: 19 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 32% helix, 23% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	L-asparaginase 1 (EC 3.5.1.1)	protein	326	33% helix, 23% strand	P0A962
B	L-asparaginase 1 (EC 3.5.1.1)	protein	336	32% helix, 22% strand	P0A962
C	L-asparaginase 1 (EC 3.5.1.1)	protein	323	32% helix, 24% strand	P0A962
D	L-asparaginase 1 (EC 3.5.1.1)	protein	334	30% helix, 23% strand	P0A962

Ligands and binding sites

ASN · Asparagine · ligand · 4 copies · chains A, C, B, D
CL · Chloride ion · ion · 10 copies · chains A, C, B, D
EDO · 1,2-ethanediol · additive · 11 copies · chains A, C, B, D
CIT · Citric acid · additive · 4 copies · chains A, C, B, D
GOL · Glycerol · additive · chains A, B, C

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

Pockets

19 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	254	0.84	0.96	45	EDO, ASN
2	243	0.84	0.96	52	ASN, EDO
3	212	0.77	0.91	39	empty
4	133	0.77	0.95	28	empty
5	649	0.73	0.80	87	CL

Interfaces

6 interfaces between chains.

B–D · 2094 Å² buried · 28 hydrogen bonds · protein-protein
A–C · 1762 Å² buried · 24 hydrogen bonds · protein-protein
C–D · 1224 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1197 Å² buried · 16 hydrogen bonds · protein-protein
B–C · 222 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (additive adduct).

Compared structures

6NXC · ECAI(T162A) mutant in complex with citrate at pH 4 · the same entry in another collection · chain B against B, TM-score 1.00
P0A962 · AlphaFold monomer V2.0 prediction for L-asparaginase 1 (P0A962) · a predicted model of the same protein · chain C 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 P0A962
Elsewhere: RCSB PDB 6NXC · PDBe 6NXC · UniProt P0A962

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