MolNFT v1 · #52322 · protein

H. halophila dodecin in complex with riboflavin

2VXA: “H. halophila dodecin in complex with riboflavin”. X-ray diffraction, 2 ligands (RBF, CL), 16 pockets (best druggability 0.77). MolNFT v1 #52322 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2VXA
Type: protein
Length: 792 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Dodecin
UniProt: A1WUH0
Ligands: RBF, CL
Pockets: 16 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 23% helix, 61% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H, I, J, K, L	Dodecin	protein	66	23% helix, 61% strand	A1WUH0

Ligands and binding sites

RBF · Riboflavin · ligand · 12 copies · chains A, C, E, B, K, G, D, F, I, L, H, J
CL · Chloride ion · ion · 24 copies · chains A, B, C, H, E, F, D, L, G, I, J, K

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

Pockets

16 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1003	0.77	0.79	85	RBF, CL
2	481	0.70	0.80	40	CL, RBF
3	467	0.69	0.80	35	RBF, CL
4	488	0.68	0.79	39	RBF, CL
5	472	0.68	0.79	41	CL, RBF

Interfaces

30 interfaces between chains.

C–F · 590 Å² buried · 9 hydrogen bonds · protein-protein
F–G · 581 Å² buried · 9 hydrogen bonds · protein-protein
D–I · 580 Å² buried · 9 hydrogen bonds · protein-protein
I–J · 580 Å² buried · 9 hydrogen bonds · protein-protein
E–L · 580 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

2VXA · H. halophila dodecin in complex with riboflavin · the same entry in another collection · chain I against I, 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 A1WUH0
Elsewhere: RCSB PDB 2VXA · PDBe 2VXA · UniProt A1WUH0

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