MolNFT v1 · #154420 · protein

Crystal structure of fkrp in complex with mg ion and cmp

6KAL · Fukutin-related protein: “Crystal structure of fkrp in complex with mg ion and cmp”. X-ray diffraction, 4 ligands (C5P, NAG, MG), 20 pockets (best druggability 0.83). MolNFT v1 #154420 on GenesisL1: 3D structure, binding sites and…

PDB: 6KAL
Type: protein
Length: 1,772 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fukutin-related protein
UniProt: Q9H9S5
Ligands: C5P, NAG, MG, ZN
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 4 distinct chains · 29% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fukutin-related protein	protein	443	30% helix, 28% strand	Q9H9S5
B	Fukutin-related protein	protein	445	29% helix, 26% strand	Q9H9S5
C	Fukutin-related protein	protein	441	29% helix, 27% strand	Q9H9S5
D	Fukutin-related protein	protein	443	29% helix, 27% strand	Q9H9S5

Ligands and binding sites

C5P · Cytidine-5'-monophosphate · ligand · 4 copies · chains A, B, C, D
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, B, C, D
MG · Magnesium ion · metal · 8 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, 17 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1072	0.83	0.84	97	empty
2	567	0.74	0.82	48	empty
3	620	0.73	0.80	51	empty
4	713	0.73	0.79	46	empty
5	530	0.73	0.81	52	empty

Interfaces

6 interfaces between chains.

C–D · 1524 Å² buried · 22 hydrogen bonds · protein-protein
A–B · 1492 Å² buried · 21 hydrogen bonds · protein-protein
A–C · 840 Å² buried · 7 hydrogen bonds · protein-protein
B–D · 692 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 83 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 glycan, 4 disulfide, 1 covalent (N-glycosylation, disulfide, covalent ligand).

Compared structures

6KAL · Crystal structure of FKRP in complex with Mg ion and CMP · 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 6KAL · PDBe 6KAL · UniProt Q9H9S5

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