MolNFT v1 · #154419 · protein

Crystal structure of fkrp in complex with mg ion

6KAK · Fukutin-related protein: “Crystal structure of fkrp in complex with mg ion”. X-ray diffraction, 3 ligands (NAG, MG, ZN), 20 pockets (best druggability 0.79). MolNFT v1 #154419 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 6KAK
Type: protein
Length: 1,753 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fukutin-related protein
UniProt: Q9H9S5
Ligands: NAG, MG, ZN
Pockets: 20 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 30% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fukutin-related protein	protein	443	31% helix, 27% strand	Q9H9S5
B	Fukutin-related protein	protein	439	29% helix, 27% strand	Q9H9S5
C	Fukutin-related protein	protein	441	31% helix, 26% strand	Q9H9S5
D	Fukutin-related protein	protein	430	30% helix, 27% strand	Q9H9S5

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, C, B, D
MG · Magnesium ion · metal · 7 copies · chains A, B, C, D
ZN · Zinc 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, 16 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	502	0.79	0.86	54	empty
2	591	0.75	0.81	52	empty
3	578	0.74	0.81	45	empty
4	738	0.73	0.79	47	empty
5	576	0.73	0.81	49	empty

Interfaces

6 interfaces between chains.

A–B · 1558 Å² buried · 23 hydrogen bonds · protein-protein
C–D · 1528 Å² buried · 23 hydrogen bonds · protein-protein
A–C · 823 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 700 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 103 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6KAK · Crystal structure of FKRP in complex with Mg 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 D against A, TM-score 0.99

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 6KAK · PDBe 6KAK · UniProt Q9H9S5

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