MolNFT v1 · #25133 · protein

Crystal structure of tetrameric kaib from T.ELONGATUS bp-1

1VGL · Circadian clock protein kaib: “Crystal structure of tetrameric kaib from T.ELONGATUS bp-1”. X-ray diffraction, 1 ligand (HG), 3 pockets (best druggability 0.57). MolNFT v1 #25133 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 1VGL
Type: protein
Length: 404 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Circadian clock protein kaib
UniProt: Q79V61
Ligands: HG
Pockets: 3 · best druggability 0.57

Structure

x-ray diffraction · 4 distinct chains · 36% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Circadian clock protein kaib	protein	96	39% helix, 28% strand	Q79V61
B	Circadian clock protein kaib	protein	105	34% helix, 33% strand	Q79V61
C	Circadian clock protein kaib	protein	100	36% helix, 29% strand	Q79V61
D	Circadian clock protein kaib	protein	103	36% helix, 29% strand	Q79V61

Ligands and binding sites

HG · Mercury (II) ion · metal · 2 copies · chains A, C

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

Pockets

3 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	192	0.57	0.80	21	empty
2	52	0.31	0.76	17	empty
3	56	0.28	0.74	16	empty

Interfaces

3 interfaces between chains.

A–B · 808 Å² buried · 10 hydrogen bonds · protein-protein
C–D · 801 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 342 Å² buried · 2 hydrogen bonds · protein-protein

Compared structures

1VGL · Crystal structure of tetrameric KaiB from T.elongatus BP-1 · the same entry in another collection · chain D against D, TM-score 1.00
Q79V61 · AlphaFold monomer V2.0 prediction for circadian clock protein kaib (Q79V61) · a predicted model of the same protein · chain C against A, TM-score 0.49

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 Q79V61
Elsewhere: RCSB PDB 1VGL · PDBe 1VGL · UniProt Q79V61

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