MolNFT v1 · #163816 · protein

Crystal structure of ancestral flavin-containing monooxygenase (fmo) 3-6

6SE3: “Crystal structure of ancestral flavin-containing monooxygenase (fmo) 3-6”. X-ray diffraction, 3 ligands (FAD, NAP, OXY), 20 pockets (best druggability 0.85). MolNFT v1 #163816 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6SE3
Type: protein
Length: 3,168 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ancestral flavin-containing monooxygenase (fmo) 3-6
Ligands: FAD, NAP, OXY
Pockets: 20 · best druggability 0.85

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, A, B, C, E, F	Ancestral flavin-containing monooxygenase (fmo) 3-6	protein	528	35% helix, 17% strand	—

Ligands and binding sites

FAD · Flavin-adenine dinucleotide · ligand · 6 copies · chains D, A, B, C, E, F
NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains D, A, B, C, E, F
OXY · Oxygen molecule · ion · 6 copies · chains D, A, B, C, E, F

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	630	0.85	0.90	82	empty
2	631	0.85	0.90	73	empty
3	1075	0.85	0.86	99	FAD, NAP, OXY
4	1093	0.85	0.86	103	FAD, NAP, OXY
5	1117	0.85	0.86	96	FAD, NAP, OXY

Interfaces

9 interfaces between chains.

A–E · 2165 Å² buried · 42 hydrogen bonds · protein-protein
C–F · 2137 Å² buried · 42 hydrogen bonds · protein-protein
D–B · 2123 Å² buried · 40 hydrogen bonds · protein-protein
B–C · 339 Å² buried · 0 hydrogen bonds · protein-protein
D–F · 335 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

6SE3 · Crystal Structure of Ancestral Flavin-containing monooxygenase (FMO) 3-6 · the same entry in another collection · chain D against D, 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
Elsewhere: RCSB PDB 6SE3 · PDBe 6SE3

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