MolNFT v1 · #158260 · protein

Structure of cyanthece apo mcda

6NON · Cobyrinic acid ac-diamide synthase: “Structure of cyanthece apo mcda”. X-ray diffraction, 2 ligands (ADP, MG), 4 pockets (best druggability 0.51). MolNFT v1 #158260 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6NON
Type: protein
Length: 511 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cobyrinic acid ac-diamide synthase
UniProt: B7KMS4
Ligands: ADP, MG
Pockets: 4 · best druggability 0.51

Structure

x-ray diffraction · 2 distinct chains · 47% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cobyrinic acid ac-diamide synthase	protein	259	46% helix, 17% strand	B7KMS4
B	Cobyrinic acid ac-diamide synthase	protein	252	47% helix, 18% strand	B7KMS4

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains B
MG · Magnesium ion · metal · chains B

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	91	0.51	0.83	21	empty
2	140	0.43	0.75	22	ADP, MG
3	73	0.32	0.74	14	empty
4	68	0.30	0.74	13	empty

Interfaces

1 interface between chains.

A–B · 644 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (engineered).

Compared structures

6NON · Structure of Cyanthece apo McdA · 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 B7KMS4
Elsewhere: RCSB PDB 6NON · PDBe 6NON · UniProt B7KMS4

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