MolNFT v1 · #95898 · protein

Pyld holoenzyme

4J43: “Pyld holoenzyme”. X-ray diffraction, 3 ligands (NAD, NA, MG), 3 pockets (best druggability 0.63). MolNFT v1 #95898 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4J43
Type: protein
Length: 504 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyld
EC: 1.4.1.-
UniProt: Q46E80
Ligands: NAD, NA, MG
Pockets: 3 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Pyld (EC 1.4.1.-)	protein	251	43% helix, 20% strand	Q46E80
B	Pyld (EC 1.4.1.-)	protein	253	41% helix, 20% strand	Q46E80

Ligands and binding sites

NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
NA · Sodium ion · metal · 2 copies · chains A, B
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

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	414	0.63	0.77	52	empty
2	202	0.49	0.76	40	NAD, MG
3	188	0.47	0.75	28	NAD, MG

Interfaces

1 interface between chains.

A–B · 519 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

4J43 · PylD holoenzyme · 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 Q46E80
Elsewhere: RCSB PDB 4J43 · PDBe 4J43 · UniProt Q46E80

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