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CYCLODEAMINASE_PA

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

PDB: 5GZL
Type: protein
Length: 704 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysine cyclodeaminase
EC: 4.3.1.12
UniProt: D9UBW0
Ligands: NAD, LYS
Pockets: 3 · best druggability 0.78

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Lysine cyclodeaminase (EC 4.3.1.12)	protein	347	38% helix, 22% strand	D9UBW0
A	Lysine cyclodeaminase (EC 4.3.1.12)	protein	357	37% helix, 21% strand	D9UBW0

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains B, A
LYS · Lysine · ligand · 2 copies · chains B, A

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

Pockets

3 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	294	0.78	0.90	51	NAD
2	328	0.74	0.86	54	NAD
3	50	0.31	0.77	13	empty

Interfaces

1 interface between chains.

B–A · 3442 Å² buried · 33 hydrogen bonds · protein-protein

Compared structures

5GZL · Cyclodeaminase_PA · the same entry in another collection · chain B against B, TM-score 1.00

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 D9UBW0
Elsewhere: RCSB PDB 5GZL · PDBe 5GZL · UniProt D9UBW0

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