MolNFT v1 · #62784 · protein

Structure of the rebeccamycin biosynthetic enzyme rebc with reduced flavin

3EPT: “Structure of the rebeccamycin biosynthetic enzyme rebc with reduced flavin”. X-ray diffraction, 2 ligands (FDA, NA), 8 pockets (best druggability 0.83). MolNFT v1 #62784 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3EPT
Type: protein
Length: 1,036 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Rebc
UniProt: Q8KI25
Ligands: FDA, NA
Pockets: 8 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 32% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Rebc	protein	516	32% helix, 25% strand	Q8KI25
B	Rebc	protein	520	32% helix, 24% strand	Q8KI25

Ligands and binding sites

FDA · Dihydroflavine-adenine dinucleotide · ligand · 2 copies · chains A, B
NA · Sodium ion · metal · chains A

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

Pockets

8 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	1138	0.83	0.83	115	NA, FDA
2	1104	0.82	0.83	111	FDA
3	77	0.75	0.98	22	empty
4	75	0.74	0.98	24	empty
5	417	0.60	0.76	33	empty

Interfaces

1 interface between chains.

A–B · 217 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

3EPT · Structure of the rebeccamycin biosynthetic enzyme RebC with reduced flavin · 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 Q8KI25
Elsewhere: RCSB PDB 3EPT · PDBe 3EPT · UniProt Q8KI25

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