MolNFT v1 · #2796 · protein

Crystal structure of cystalysin from treponema denticola contains a pyridoxal 5'-phosphate cofactor

1C7N: “Crystal structure of cystalysin from treponema denticola contains a pyridoxal 5'-phosphate cofactor”. X-ray diffraction, 1 ligand (PLP), 20 pockets (best druggability 0.84). MolNFT v1 #2796 on GenesisL1: 3D structure, binding sites…

PDB: 1C7N
Type: protein
Length: 3,152 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cystalysin
UniProt: Q56257
Ligands: PLP
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Cystalysin	protein	394	47% helix, 15% strand	Q56257

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	948	0.84	0.85	123	PLP
2	965	0.83	0.84	131	PLP
3	873	0.83	0.85	121	PLP
4	878	0.82	0.84	112	PLP
5	359	0.55	0.74	29	empty

Interfaces

7 interfaces between chains.

C–D · 1989 Å² buried · 25 hydrogen bonds · protein-protein
G–H · 1978 Å² buried · 25 hydrogen bonds · protein-protein
E–F · 1955 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 1935 Å² buried · 27 hydrogen bonds · protein-protein
F–H · 175 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 8 cofactor (pyridoxal phosphate Schiff base).

Compared structures

1C7N · Crystal structure of cystalysin from treponema denticola contains a pyridoxal… · the same entry in another collection · chain D against D, 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 Q56257
Elsewhere: RCSB PDB 1C7N · PDBe 1C7N · UniProt Q56257

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