MolNFT v1 · #51089 · protein

Crystal structure of the T. thermophilus dodecin R65A mutant

2UX9: “Crystal structure of the T. thermophilus dodecin R65A mutant”. X-ray diffraction, 4 ligands (FMN, COA, NA), 4 pockets (best druggability 0.61). MolNFT v1 #51089 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2UX9
Type: protein
Length: 404 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dodecin
UniProt: Q5SIE3
Ligands: FMN, COA, NA, PO4
Pockets: 4 · best druggability 0.61

Structure

x-ray diffraction · 3 distinct chains · 22% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Dodecin	protein	66	23% helix, 58% strand	Q5SIE3
B, E	Dodecin	protein	67	22% helix, 57% strand	Q5SIE3
C, D, F	Dodecin	protein	68	22% helix, 56% strand	Q5SIE3

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · 6 copies · chains A, C, B, D, F, E
COA · Coenzyme A · ligand · 6 copies · chains A, E, B, F, C, D
NA · Sodium ion · metal · 4 copies · chains A, C, F
PO4 · Phosphate ion · ion · 3 copies · chains B, F, C

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	281	0.61	0.79	30	FMN
2	123	0.41	0.76	23	empty
3	94	0.40	0.77	12	empty
4	53	0.31	0.76	12	empty

Interfaces

9 interfaces between chains.

D–E · 620 Å² buried · 8 hydrogen bonds · protein-protein
A–F · 612 Å² buried · 10 hydrogen bonds · protein-protein
B–D · 610 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 609 Å² buried · 9 hydrogen bonds · protein-protein
C–F · 609 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

2UX9 · Crystal structure of the T. thermophilus dodecin R65A mutant · the same entry in another collection · chain F against F, TM-score 1.00
Q5SIE3 · AlphaFold monomer V2.0 prediction for dodecin (Q5SIE3) · a predicted model of the same protein · chain C against A, TM-score 0.96

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 Q5SIE3
Elsewhere: RCSB PDB 2UX9 · PDBe 2UX9 · UniProt Q5SIE3

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