MolNFT v1 · #158262 · protein

Structure of cyanothece MCDA(D38A)-ATP complex

6NOP · Cobyrinic acid ac-diamide synthase: “Structure of cyanothece MCDA(D38A)-ATP complex”. X-ray diffraction, 2 ligands (ATP, MG), 4 pockets (best druggability 0.86). MolNFT v1 #158262 on GenesisL1: 3D structure, binding sites and…

PDB: 6NOP
Type: protein
Length: 522 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cobyrinic acid ac-diamide synthase
UniProt: B7KMS4
Ligands: ATP, MG
Pockets: 4 · best druggability 0.86

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Cobyrinic acid ac-diamide synthase	protein	262	45% helix, 17% strand	B7KMS4
A	Cobyrinic acid ac-diamide synthase	protein	260	46% helix, 17% strand	B7KMS4

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains B, A
MG · Magnesium ion · metal · 2 copies · chains B, A

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

Pockets

4 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	603	0.86	0.91	78	ATP, MG
2	166	0.42	0.73	28	empty
3	101	0.37	0.74	20	empty
4	92	0.37	0.75	20	empty

Interfaces

1 interface between chains.

B–A · 1188 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

6NOP · Structure of Cyanothece McdA(D38A)-ATP complex · the same entry in another collection · chain B against B, 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 B7KMS4
Elsewhere: RCSB PDB 6NOP · PDBe 6NOP · UniProt B7KMS4

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