MolNFT v1 · #165955 · protein

Structure of dynf from the dynemicin biosynthesis pathway of micromonospora chersina

6UBL: “Structure of dynf from the dynemicin biosynthesis pathway of micromonospora chersina”. X-ray diffraction, 1 ligand (PLM), 7 pockets (best druggability 0.84). MolNFT v1 #165955 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6UBL
Type: protein
Length: 422 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dynf
UniProt: B2BM43
Ligands: PLM
Pockets: 7 · best druggability 0.84

Structure

x-ray diffraction · 1 distinct chain · 4% helix, 49% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Dynf	protein	211	4% helix, 49% strand	B2BM43

Ligands and binding sites

PLM · Palmitic acid · ligand · 2 copies · chains A, B

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

Pockets

7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	191	0.84	0.97	30	PLM
2	188	0.83	0.97	31	PLM
3	66	0.54	0.87	19	empty
4	87	0.43	0.79	15	empty
5	71	0.34	0.76	13	empty

Interfaces

1 interface between chains.

A–B · 1871 Å² buried · 38 hydrogen bonds · protein-protein

Compared structures

6UBL · Structure of DynF from the Dynemicin Biosynthesis Pathway of Micromonospora chersina · 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 B2BM43
Elsewhere: RCSB PDB 6UBL · PDBe 6UBL · UniProt B2BM43

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