MolNFT v1 · #121404 · protein

Crystal structure of nadc deletion mutant in C2221 space group

5HUO · Nicotinate-nucleotide diphosphorylase (carboxylating): “Crystal structure of nadc deletion mutant in C2221 space group”. X-ray diffraction, 1 ligand (SO4), 20 pockets (best druggability 0.73). MolNFT v1 #121404 on GenesisL1: 3D…

PDB: 5HUO
Type: protein
Length: 1,694 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nicotinate-nucleotide diphosphorylase (carboxylating)
EC: 2.4.2.19
UniProt: A0A0H3BVM1
Ligands: SO4
Pockets: 20 · best druggability 0.73

Structure

x-ray diffraction · 5 distinct chains · 42% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Nicotinate-nucleotide diphosphorylase (carboxylating) (EC 2.4.2.19)	protein	283	43% helix, 20% strand	A0A0H3BVM1
C	Nicotinate-nucleotide diphosphorylase (carboxylating) (EC 2.4.2.19)	protein	280	42% helix, 20% strand	A0A0H3BVM1
E	Nicotinate-nucleotide diphosphorylase (carboxylating) (EC 2.4.2.19)	protein	282	42% helix, 20% strand	A0A0H3BVM1
F	Nicotinate-nucleotide diphosphorylase (carboxylating) (EC 2.4.2.19)	protein	284	43% helix, 20% strand	A0A0H3BVM1
H	Nicotinate-nucleotide diphosphorylase (carboxylating) (EC 2.4.2.19)	protein	282	41% helix, 19% strand	A0A0H3BVM1

Ligands and binding sites

SO4 · Sulfate ion · ion · 20 copies · chains A, E, B, H, C, F

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

Pockets

20 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	402	0.73	0.84	50	SO4
2	400	0.72	0.83	48	SO4
3	581	0.71	0.80	50	SO4
4	438	0.71	0.82	61	SO4
5	553	0.64	0.76	59	empty

Interfaces

6 interfaces between chains.

B–H · 2808 Å² buried · 62 hydrogen bonds · protein-protein
C–E · 2554 Å² buried · 57 hydrogen bonds · protein-protein
A–E · 1019 Å² buried · 5 hydrogen bonds · protein-protein
B–F · 969 Å² buried · 6 hydrogen bonds · protein-protein
F–H · 636 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

5HUO · Crystal Structure of NadC Deletion Mutant in C2221 Space Group · 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 A0A0H3BVM1
Elsewhere: RCSB PDB 5HUO · PDBe 5HUO · UniProt A0A0H3BVM1

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