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Structure of bacillus subtilis nicotinic acid mononucleotide adenylyl transferase

Analyse Structure of bacillus subtilis nicotinic acid mononucleotide adenylyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1KAQ
Type: protein
Length: 1,087 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Nicotinate-nucleotide adenylyltransferase
EC: 2.7.7.18
UniProt: P54455
Ligands: DND
Pockets: 14 · best druggability 0.79

Structure

x-ray diffraction · 3 distinct chains · 36% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Nicotinate-nucleotide adenylyltransferase (EC 2.7.7.18)	protein	186	36% helix, 16% strand	P54455
E	Nicotinate-nucleotide adenylyltransferase (EC 2.7.7.18)	protein	176	36% helix, 17% strand	P54455
F	Nicotinate-nucleotide adenylyltransferase (EC 2.7.7.18)	protein	167	35% helix, 17% strand	P54455

Ligands and binding sites

DND · Nicotinic acid adenine dinucleotide · ligand · 6 copies · chains F, E, D, C, B, A

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

Pockets

14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	399	0.79	0.88	51	DND
2	390	0.79	0.88	50	DND
3	381	0.78	0.88	49	DND
4	362	0.77	0.88	45	DND
5	344	0.68	0.81	39	DND

Interfaces

6 interfaces between chains.

A–D · 1009 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 1006 Å² buried · 9 hydrogen bonds · protein-protein
E–F · 964 Å² buried · 6 hydrogen bonds · protein-protein
A–B · 886 Å² buried · 17 hydrogen bonds · protein-protein
A–C · 79 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

1KAQ · Structure of Bacillus subtilis Nicotinic Acid Mononucleotide Adenylyl Transferase · the same entry in another collection · chain F against F, TM-score 1.00
P54455 · AlphaFold monomer V2.0 prediction for nicotinate-nucleotide adenylyltransferase (P54455) · a predicted model of the same protein · chain F against A, TM-score 0.98

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 P54455
Elsewhere: RCSB PDB 1KAQ · PDBe 1KAQ · UniProt P54455

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