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Crystal structure of kaib from synechocystis sp.

Analyse Crystal structure of kaib from synechocystis sp. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1WWJ
Type: protein
Length: 386 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Circadian clock protein kaib
UniProt: P74645
Ligands: MLT, BET
Pockets: 3 · best druggability 0.43

Structure

x-ray diffraction · 3 distinct chains · 36% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Circadian clock protein kaib	protein	99	38% helix, 29% strand	P74645
B	Circadian clock protein kaib	protein	91	38% helix, 27% strand	P74645
C, D	Circadian clock protein kaib	protein	98	33% helix, 32% strand	P74645

Ligands and binding sites

MLT · D-malate · ligand · 8 copies · chains A, B, C, D
BET · Trimethyl glycine · ligand · 5 copies · chains A, D, B, C
IMD · Imidazole · additive · 3 copies · chains B, C, D

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	89	0.43	0.79	19	MLT
2	144	0.42	0.74	28	empty
3	96	0.40	0.77	23	empty

Interfaces

5 interfaces between chains.

A–D · 966 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 824 Å² buried · 10 hydrogen bonds · protein-protein
A–B · 767 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 681 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 586 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

1WWJ · crystal structure of KaiB from Synechocystis sp. · the same entry in another collection · chain D against D, TM-score 1.00
P74645 · AlphaFold monomer V2.0 prediction for circadian clock protein kaib (P74645) · a predicted model of the same protein · chain B against A, TM-score 0.47

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 P74645
Elsewhere: RCSB PDB 1WWJ · PDBe 1WWJ · UniProt P74645

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