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Crystal structure of the T. thermophilus dodecin in complex with prebound FMN

Analyse Crystal structure of the T. thermophilus dodecin in complex with prebound FMN in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2V21
Type: protein
Length: 402 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical protein TTHA1431
UniProt: Q5SIE3
Ligands: FMN, NA
Pockets: 4 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 22% helix, 57% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Hypothetical protein TTHA1431	protein	67	22% helix, 57% strand	Q5SIE3

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · 3 copies · chains A, B, C, D, F
NA · Sodium ion · metal · 2 copies · chains A, B, C, D, E, F

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	329	0.63	0.79	30	empty
2	97	0.40	0.77	13	empty
3	90	0.40	0.77	12	empty
4	60	0.34	0.77	15	empty

Interfaces

9 interfaces between chains.

D–F · 619 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 618 Å² buried · 7 hydrogen bonds · protein-protein
E–F · 618 Å² buried · 8 hydrogen bonds · protein-protein
D–E · 617 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 612 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

2V21 · Crystal structure of the T. thermophilus dodecin in complex with prebound FMN · 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 B 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 2V21 · PDBe 2V21 · UniProt Q5SIE3

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