MolNFT v1 · #121405 · protein

Crystal structure of nadc from streptococcus pyogenes

5HUP · Nicotinate-nucleotide pyrophosphorylase (carboxylating): “Crystal structure of nadc from streptococcus pyogenes”. X-ray diffraction, 1 ligand (SO4), 17 pockets (best druggability 0.74). MolNFT v1 #121405 on GenesisL1: 3D structure…

PDB: 5HUP
Type: protein
Length: 1,703 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nicotinate-nucleotide pyrophosphorylase (carboxylating)
EC: 2.4.2.19
UniProt: Q1J647
Ligands: SO4
Pockets: 17 · best druggability 0.74

Structure

x-ray diffraction · 4 distinct chains · 41% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, H	Nicotinate-nucleotide pyrophosphorylase (carboxylating) (EC 2.4.2.19)	protein	285	41% helix, 20% strand	Q1J647
C	Nicotinate-nucleotide pyrophosphorylase (carboxylating) (EC 2.4.2.19)	protein	280	41% helix, 20% strand	Q1J647
E	Nicotinate-nucleotide pyrophosphorylase (carboxylating) (EC 2.4.2.19)	protein	284	42% helix, 20% strand	Q1J647
F	Nicotinate-nucleotide pyrophosphorylase (carboxylating) (EC 2.4.2.19)	protein	284	42% helix, 20% strand	Q1J647

Ligands and binding sites

SO4 · Sulfate ion · ion · 17 copies · chains A, E, B, C, F, H

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

Pockets

17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	518	0.74	0.83	44	SO4
2	634	0.74	0.81	44	SO4
3	669	0.72	0.79	48	SO4
4	396	0.70	0.82	45	SO4
5	787	0.68	0.75	80	empty

Interfaces

6 interfaces between chains.

B–H · 2653 Å² buried · 44 hydrogen bonds · protein-protein
C–E · 2456 Å² buried · 38 hydrogen bonds · protein-protein
A–E · 981 Å² buried · 7 hydrogen bonds · protein-protein
B–F · 952 Å² buried · 5 hydrogen bonds · protein-protein
F–H · 598 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5HUP · Crystal Structure of NadC from Streptococcus pyogenes · 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 Q1J647
Elsewhere: RCSB PDB 5HUP · PDBe 5HUP · UniProt Q1J647

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