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Structure of amide bond synthetase mcba K483A mutant from marinactinospora thermotolerans

Analyse Structure of amide bond synthetase mcba K483A mutant from marinactinospora… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6H1B
Type: protein
Length: 2,436 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fatty acid CoA ligase
UniProt: R4R1U5
Ligands: AMP, EQ2
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 5 distinct chains · 32% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fatty acid CoA ligase	protein	487	32% helix, 29% strand	R4R1U5
B	Fatty acid CoA ligase	protein	485	32% helix, 28% strand	R4R1U5
C	Fatty acid CoA ligase	protein	490	32% helix, 28% strand	R4R1U5
D	Fatty acid CoA ligase	protein	487	32% helix, 29% strand	R4R1U5
E	Fatty acid CoA ligase	protein	487	31% helix, 29% strand	R4R1U5

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · 5 copies · chains A, B, C, D, E
EQ2 · 1-ethanoyl-9~{H}-pyrido[3,4-b]indole-3-carboxylic acid · 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, 12 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1133	0.85	0.85	105	AMP, EQ2
2	1138	0.83	0.84	105	AMP, EQ2
3	1118	0.82	0.83	128	empty
4	1179	0.81	0.83	107	AMP, EQ2
5	1175	0.81	0.82	101	AMP, EQ2

Interfaces

9 interfaces between chains.

B–C · 840 Å² buried · 19 hydrogen bonds · protein-protein
A–C · 838 Å² buried · 8 hydrogen bonds · protein-protein
A–D · 792 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 748 Å² buried · 8 hydrogen bonds · protein-protein
A–B · 493 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6H1B · Structure of amide bond synthetase Mcba K483A mutant 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 6H1B · PDBe 6H1B · UniProt R4R1U5

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