MolNFT v1 · #164198 · protein

Structure of amide bond synthetase mcba from marinactinospora thermotolerans

6SQ8 · Fatty acid CoA ligase: “Structure of amide bond synthetase mcba from marinactinospora thermotolerans”. X-ray diffraction, 2 ligands (EQ2, AMP), 20 pockets (best druggability 0.85). MolNFT v1 #164198 on GenesisL1: 3D structure…

PDB: 6SQ8
Type: protein
Length: 2,450 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fatty acid CoA ligase
UniProt: R4R1U5
Ligands: EQ2, AMP
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 5 distinct chains · 32% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fatty acid CoA ligase	protein	486	33% helix, 29% strand	R4R1U5
B	Fatty acid CoA ligase	protein	494	32% helix, 28% strand	R4R1U5
C	Fatty acid CoA ligase	protein	489	34% helix, 28% strand	R4R1U5
D	Fatty acid CoA ligase	protein	487	32% helix, 29% strand	R4R1U5
E	Fatty acid CoA ligase	protein	494	31% helix, 29% strand	R4R1U5

Ligands and binding sites

EQ2 · 1-ethanoyl-9~{H}-pyrido[3,4-b]indole-3-carboxylic acid · ligand · 5 copies · chains A, B, C, D, E
AMP · Adenosine monophosphate · ligand · 5 copies · chains A, B, C, D, E

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	979	0.85	0.86	92	EQ2, AMP
2	1105	0.84	0.85	104	EQ2, AMP
3	1070	0.84	0.85	101	EQ2, AMP
4	1059	0.84	0.84	102	EQ2, AMP
5	896	0.83	0.85	88	EQ2, AMP

Interfaces

9 interfaces between chains.

A–C · 850 Å² buried · 9 hydrogen bonds · protein-protein
A–D · 816 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 785 Å² buried · 15 hydrogen bonds · protein-protein
B–D · 769 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 512 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6SQ8 · Structure of amide bond synthetase McbA from Marinactinospora thermotolerans · 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 R4R1U5
Elsewhere: RCSB PDB 6SQ8 · PDBe 6SQ8 · UniProt R4R1U5

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.