MolNFT v1 · #126880 · protein

A multi-component acyltransferase phlabc from pseudomonas protegens soaked with the monoacetylphloroglucinol (mapg)

5MG5 · Hydroxymethylglutaryl-CoA synthase: “A multi-component acyltransferase phlabc from pseudomonas protegens soaked with the monoacetylphloroglucinol…”. X-ray diffraction, 2 ligands (13X, ZN), 20 pockets (best druggability 0.89). MolNFT…

PDB: 5MG5
Type: protein
Length: 7,194 residues
Chains: 24
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hydroxymethylglutaryl-CoA synthase; 2,4-diacetylphloroglucinol biosynthesis protein…
UniProt: A0A1Z3SPL2, A0A1Z3SPP2, Q4K420
Ligands: 13X, ZN
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 5 distinct chains · 36% helix, 22% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, P, S	Hydroxymethylglutaryl-CoA synthase	protein	358	36% helix, 25% strand	A0A1Z3SPL2
B, E, H, K, N, Q, T, W	2,4-diacetylphloroglucinol biosynthesis protein	protein	145	8% helix, 39% strand	A0A1Z3SPP2
C, F, R	2,4-diacetylphloroglucinol biosynthesis protein phlc	protein	395	39% helix, 17% strand	Q4K420
D, G, J, M, V	Hydroxymethylglutaryl-CoA synthase	protein	359	37% helix, 25% strand	A0A1Z3SPL2
I, L, O, U, X	2,4-diacetylphloroglucinol biosynthesis protein phlc	protein	396	40% helix, 17% strand	Q4K420

Ligands and binding sites

13X · benzene-1,3,5-triol · ligand · 4 copies · chains C, L, O, R
ZN · Zinc ion · metal · 8 copies · chains B, E, H, K, N, Q, T, W

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1169	0.89	0.91	130	empty
2	1109	0.89	0.91	113	empty
3	772	0.82	0.85	101	empty
4	376	0.82	0.90	63	13X
5	583	0.81	0.87	64	empty

Interfaces

97 interfaces between chains.

I–U · 2522 Å² buried · 40 hydrogen bonds · protein-protein
R–X · 2479 Å² buried · 36 hydrogen bonds · protein-protein
C–L · 2452 Å² buried · 37 hydrogen bonds · protein-protein
F–O · 2451 Å² buried · 34 hydrogen bonds · protein-protein
J–M · 2392 Å² buried · 54 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 modified (acetylation).

Compared structures

5MG5 · A multi-component acyltransferase PhlABC from Pseudomonas protegens soaked with the… · 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 A0A1Z3SPL2
Every structure of UniProt A0A1Z3SPP2
Every structure of UniProt Q4K420
Elsewhere: RCSB PDB 5MG5 · PDBe 5MG5 · UniProt A0A1Z3SPL2 · UniProt A0A1Z3SPP2 · UniProt Q4K420

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