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Crystal structure of succinyl diaminopimelate desuccinylase

Analyse Crystal structure of succinyl diaminopimelate desuccinylase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1VGY
Type: protein
Length: 750 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Succinyl-diaminopimelate desuccinylase
UniProt: Q9JYL2
Pockets: 4 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Succinyl-diaminopimelate desuccinylase	protein	375	31% helix, 28% strand	Q9JYL2

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	320	0.58	0.77	42	empty
2	317	0.57	0.77	41	empty
3	118	0.36	0.73	32	empty
4	88	0.31	0.72	25	empty

Interfaces

1 interface between chains.

A–B · 1628 Å² buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 modified (engineered).

Compared structures

1VGY · Crystal structure of succinyl diaminopimelate desuccinylase · the same entry in another collection · chain A against A, TM-score 1.00
Q9JYL2 · AlphaFold monomer V2.0 prediction for succinyl-diaminopimelate desuccinylase (Q9JYL2) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q9JYL2
Elsewhere: RCSB PDB 1VGY · PDBe 1VGY · UniProt Q9JYL2

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