MolNFT v1 · #154418 · protein

Crystal structure of fkrp in complex with ba ion

6KAJ · Fukutin-related protein: “Crystal structure of fkrp in complex with ba ion”. X-ray diffraction, 5 ligands (CDP, RB0, NAG), 20 pockets (best druggability 0.84). MolNFT v1 #154418 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6KAJ
Type: protein
Length: 1,779 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fukutin-related protein
EC: 2.4.2.-
UniProt: Q9H9S5
Ligands: CDP, RB0, NAG, ZN, BA
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 29% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fukutin-related protein (EC 2.4.2.-)	protein	446	29% helix, 27% strand	Q9H9S5
B, C	Fukutin-related protein (EC 2.4.2.-)	protein	445	28% helix, 26% strand	Q9H9S5
D	Fukutin-related protein (EC 2.4.2.-)	protein	443	30% helix, 26% strand	Q9H9S5

Ligands and binding sites

CDP · Cytidine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
RB0 · D-ribitol · ligand · 4 copies · chains A, B, C, D
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, C, B, D
ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
BA · Barium ion · metal · 4 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1029	0.84	0.85	134	empty
2	596	0.75	0.82	50	empty
3	323	0.75	0.86	37	CDP, RB0, BA
4	690	0.75	0.80	46	empty
5	563	0.73	0.81	46	empty

Interfaces

5 interfaces between chains.

C–D · 1466 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1455 Å² buried · 23 hydrogen bonds · protein-protein
B–D · 721 Å² buried · 8 hydrogen bonds · protein-protein
A–C · 535 Å² buried · 1 hydrogen bond · protein-protein
B–C · 11 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 glycan, 4 disulfide (N-glycosylation, disulfide).

Compared structures

6KAJ · Crystal structure of FKRP in complex with Ba ion · the same entry in another collection · chain D against D, TM-score 1.00
Q9H9S5 · AlphaFold monomer V2.0 prediction for fukutin-related protein (Q9H9S5) · a predicted model of the same protein · chain A against A, 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 Q9H9S5
Elsewhere: RCSB PDB 6KAJ · PDBe 6KAJ · UniProt Q9H9S5

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