MolNFT v1 · #101865 · protein

Crystal structure of phycobiliprotein lyase cpct

4O4O · Phycocyanobilin lyase cpct: “Crystal structure of phycobiliprotein lyase cpct”. X-ray diffraction, 1 ligand (MG), 5 pockets (best druggability 0.82). MolNFT v1 #101865 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4O4O
Type: protein
Length: 394 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phycocyanobilin lyase cpct
EC: 4.-.-.-
UniProt: Q8YLF9
Ligands: MG
Pockets: 5 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 18% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Phycocyanobilin lyase cpct (EC 4.-.-.-)	protein	197	18% helix, 43% strand	Q8YLF9

Ligands and binding sites

MG · Magnesium ion · metal · 2 copies · chains A, B

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

Pockets

5 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	287	0.82	0.92	34	MG
2	327	0.82	0.91	34	MG
3	94	0.42	0.77	22	empty
4	61	0.33	0.77	17	empty
5	80	0.33	0.74	17	empty

Interfaces

1 interface between chains.

A–B · 1003 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 modified, 2 disulfide (engineered, disulfide).

Compared structures

4O4O · Crystal structure of phycobiliprotein lyase CpcT · the same entry in another collection · chain A against A, TM-score 1.00
Q8YLF9 · AlphaFold monomer V2.0 prediction for phycocyanobilin lyase cpct (Q8YLF9) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 Q8YLF9
Elsewhere: RCSB PDB 4O4O · PDBe 4O4O · UniProt Q8YLF9

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