MolNFT v1 · #120412 · protein

CYCLODEAMINASE_PA

5GZM · Lysine cyclodeaminase: “CYCLODEAMINASE_PA”. X-ray diffraction, 2 ligands (NAD, YCP), 3 pockets (best druggability 0.80). MolNFT v1 #120412 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5GZM
Type: protein
Length: 701 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, YCP
Pockets: 3 · best druggability 0.80

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysine cyclodeaminase (EC 4.3.1.12)	protein	355	37% helix, 21% strand	D9UBW0
B	Lysine cyclodeaminase (EC 4.3.1.12)	protein	346	40% helix, 22% strand	D9UBW0

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
YCP · (2S)-piperidine-2-carboxylic acid · ligand · 2 copies · chains A, B

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	329	0.80	0.90	50	NAD, YCP
2	343	0.79	0.89	50	NAD, YCP
3	78	0.35	0.76	17	empty

Interfaces

1 interface between chains.

A–B · 3458 Å² buried · 35 hydrogen bonds · protein-protein

Compared structures

5GZM · 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 5GZM · PDBe 5GZM · UniProt D9UBW0

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