MolNFT v1 · #63558 · protein

Crystal structure of a putative plp-dependent beta-cystathionase (aecd, DIP1736) from corynebacterium diphtheriae at 1.99 a resolution

3FDB: “Crystal structure of a putative plp-dependent beta-cystathionase (aecd, DIP1736) from corynebacterium…”. X-ray diffraction, 2 ligands (NA, CL), 3 pockets (best druggability 0.51). MolNFT v1 #63558 on GenesisL1: 3D structure, binding…

PDB: 3FDB
Type: protein
Length: 377 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Putative plp-dependent beta-cystathionase
EC: 3.-.-.-
UniProt: Q6NFZ9
Ligands: NA, CL
Pockets: 3 · best druggability 0.51

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Putative plp-dependent beta-cystathionase (EC 3.-.-.-)	protein	377	47% helix, 15% strand	Q6NFZ9

Ligands and binding sites

NA · Sodium ion · metal · chains A
CL · Chloride ion · ion · 5 copies · chains A
EDO · 1,2-ethanediol · additive · 9 copies · chains 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	259	0.51	0.74	36	CL, EDO
2	98	0.36	0.74	19	empty
3	50	0.27	0.74	15	empty

Modifications

Observed in the structure: 8 modified (engineered, cofactor).

Compared structures

3FDB · Crystal structure of a putative plp-dependent beta-cystathionase (aecd, dip1736) from… · the same entry in another collection · chain A against A, 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 Q6NFZ9
Elsewhere: RCSB PDB 3FDB · PDBe 3FDB · UniProt Q6NFZ9

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