Research workbench

Albumin binding domain fused to a mutant of the erwinia asparaginase

Analyse Albumin binding domain fused to a mutant of the erwinia asparaginase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7U6M
Type: protein
Length: 1,323 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L-asparaginase
EC: 3.5.1.1
UniProt: P06608
Ligands: ASP
Pockets: 15 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, D	L-asparaginase (EC 3.5.1.1)	protein	327	32% helix, 24% strand	P06608
C	L-asparaginase (EC 3.5.1.1)	protein	342	31% helix, 24% strand	P06608

Ligands and binding sites

ASP · Aspartic acid · ligand · 4 copies · chains A, C, B, D

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

Pockets

15 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	474	0.86	0.93	82	empty
2	306	0.78	0.89	48	ASP
3	270	0.75	0.88	45	ASP
4	254	0.74	0.88	40	ASP
5	247	0.73	0.87	46	ASP

Interfaces

6 interfaces between chains.

A–C · 2405 Å² buried · 44 hydrogen bonds · protein-protein
B–D · 2398 Å² buried · 41 hydrogen bonds · protein-protein
B–C · 1126 Å² buried · 24 hydrogen bonds · protein-protein
A–D · 1115 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 1088 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

7U6M · Albumin binding domain fused to a mutant of the Erwinia asparaginase · the same entry in another collection · chain D against D, TM-score 1.00
P06608 · AlphaFold monomer V2.0 prediction for L-asparaginase (P06608) · 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 P06608
Elsewhere: RCSB PDB 7U6M · PDBe 7U6M · UniProt P06608

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