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Ecaii in complex with citrate at pH 7

Analyse Ecaii in complex with citrate at pH 7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6NXB
Type: protein
Length: 1,276 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: 11 · best druggability 0.64

Structure

x-ray diffraction · 4 distinct chains · 34% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	L-asparaginase 2 (EC 3.5.1.1)	protein	326	33% helix, 21% strand	P00805
B	L-asparaginase 2 (EC 3.5.1.1)	protein	314	33% helix, 22% strand	P00805
C	L-asparaginase 2 (EC 3.5.1.1)	protein	315	35% helix, 22% strand	P00805
D	L-asparaginase 2 (EC 3.5.1.1)	protein	321	33% helix, 21% strand	P00805

Ligands and binding sites

CIT · Citric acid · additive · 5 copies · chains A, B, C, D
GOL · Glycerol · additive · chains A, B

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

Pockets

11 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	150	0.64	0.86	30	empty
2	118	0.64	0.88	32	empty
3	305	0.55	0.76	27	CIT
4	278	0.54	0.76	28	CIT
5	264	0.54	0.76	28	CIT

Interfaces

3 interfaces between chains.

C–D · 2066 Å² buried · 40 hydrogen bonds · protein-protein
A–B · 2049 Å² buried · 41 hydrogen bonds · protein-protein
A–C · 166 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6NXB · Ecaii 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 6NXB · PDBe 6NXB · UniProt P00805

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