MolNFT v1 · #120797 · protein

Ca. korarchaeum cryptofilum dinucleotide forming acetyl-coenzyme a synthetase 1 in complex with phosphate and coenzyme a

5HBR · Alpha subunit of acyl-CoA synthetase (ndp forming): “Ca. korarchaeum cryptofilum dinucleotide forming acetyl-coenzyme a synthetase 1 in complex with phosphate and…”. X-ray diffraction, 4 ligands (COA, MG, NA), 16 pockets (best…

PDB: 5HBR
Type: protein
Length: 1,386 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpha subunit of acyl-CoA synthetase (ndp forming); Beta subunit of acyl-CoA synthetase…
UniProt: B1L3C9, B1L7P8
Ligands: COA, MG, NA, PO4
Pockets: 16 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Alpha subunit of acyl-CoA synthetase (ndp forming)	protein	464	44% helix, 19% strand	B1L3C9
B, D	Beta subunit of acyl-CoA synthetase (ndp forming)	protein	229	38% helix, 29% strand	B1L7P8

Ligands and binding sites

COA · Coenzyme A · ligand · 2 copies · chains A, C
MG · Magnesium ion · metal · 2 copies · chains A, C
NA · Sodium ion · metal · chains A, C
PO4 · Phosphate ion · ion · 2 copies · chains A, C

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

Pockets

16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	824	0.77	0.80	91	PO4, MG
2	683	0.77	0.82	91	NA, PO4
3	975	0.73	0.76	82	empty
4	468	0.71	0.81	46	empty
5	282	0.58	0.78	39	empty

Interfaces

4 interfaces between chains.

A–C · 2030 Å² buried · 24 hydrogen bonds · protein-protein
A–B · 817 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 817 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 552 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

5HBR · Ca. Korarchaeum cryptofilum dinucleotide forming Acetyl-coenzyme A synthetase 1 in… · 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 B1L3C9
Every structure of UniProt B1L7P8
Elsewhere: RCSB PDB 5HBR · PDBe 5HBR · UniProt B1L3C9 · UniProt B1L7P8

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