MolNFT v1 · #126457 · protein

A multi-component acyltransferase phlabc from pseudomonas protegens

5M3K: “A multi-component acyltransferase phlabc from pseudomonas protegens”. X-ray diffraction, 1 ligand (ZN), 20 pockets (best druggability 0.81). MolNFT v1 #126457 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5M3K
Type: protein
Length: 1,799 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phla; 2,4-diacetylphloroglucinol biosynthesis protein phlb; 2,4-diacetylphloroglucinol…
UniProt: Q9TP23, Q4K419, Q4K420
Ligands: ZN
Pockets: 20 · best druggability 0.81

Structure

x-ray diffraction · 4 distinct chains · 31% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Phla	protein	359	36% helix, 24% strand	Q9TP23
B	2,4-diacetylphloroglucinol biosynthesis protein phlb	protein	144	10% helix, 38% strand	Q4K419
C, F	2,4-diacetylphloroglucinol biosynthesis protein phlc	protein	396	41% helix, 17% strand	Q4K420
E	2,4-diacetylphloroglucinol biosynthesis protein phlb	protein	145	10% helix, 37% strand	Q4K419

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains B, 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, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	854	0.81	0.83	89	empty
2	799	0.79	0.82	76	empty
3	1054	0.78	0.80	96	empty
4	524	0.75	0.83	69	empty
5	114	0.75	0.94	19	empty

Interfaces

11 interfaces between chains.

B–C · 1625 Å² buried · 22 hydrogen bonds · protein-protein
E–F · 1603 Å² buried · 19 hydrogen bonds · protein-protein
A–D · 1468 Å² buried · 16 hydrogen bonds · protein-protein
A–E · 1371 Å² buried · 16 hydrogen bonds · protein-protein
B–D · 1343 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (acetylation).

Compared structures

5M3K · A multi-component acyltransferase PhlABC from Pseudomonas protegens · 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 Q9TP23
Every structure of UniProt Q4K419
Every structure of UniProt Q4K420
Elsewhere: RCSB PDB 5M3K · PDBe 5M3K · UniProt Q9TP23 · UniProt Q4K419 · UniProt Q4K420

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