SMTL ID : 6l7s.1

Crystal structure of FKRP in complex with Mg ion, Zinc peak data

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.41 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.249, C.256, C.277, C.278 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.249, A:C.256, A:C.277, A:C.278 ZN.5: 4 residues within 4Å: Chain B: C.249, C.256, C.277, C.278 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.249, B:C.256, B:C.277, B:C.278 ZN.10: 5 residues within 4Å: Chain C: C.249, C.256, P.275, C.277, C.278 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.249, C:C.256, C:C.277, C:C.278 ZN.13: 4 residues within 4Å: Chain D: C.249, C.256, C.277, C.278 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.249, D:C.256, D:C.277, D:C.278

7 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.2: 4 residues within 4Å: Chain A: N.132, R.141, Y.142, G.143 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.132 NAG.3: 6 residues within 4Å: Chain A: N.169 Chain B: P.71 Chain C: L.451 Chain D: L.53, P.54, R.55 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain D Water bridges: A:N.169, A:N.169, A:R.189 Hydrogen bonds: D:L.53, D:R.55 NAG.6: 3 residues within 4Å: Chain B: N.132, R.141, G.143 No protein-ligand interaction detected (PLIP) NAG.7: 5 residues within 4Å: Chain B: E.78, A.164, R.165, F.168, N.169 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.78, B:F.168 Hydrogen bonds: B:N.169 NAG.11: 7 residues within 4Å: Chain A: L.451 Chain B: L.53, P.54, R.55 Chain C: R.165, N.169 Chain D: P.71 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Water bridges: C:N.169, C:N.169, C:R.189 Hydrogen bonds: B:L.53, B:R.55 NAG.14: 4 residues within 4Å: Chain D: N.132, R.141, Y.142, G.143 No protein-ligand interaction detected (PLIP) NAG.15: 5 residues within 4Å: Chain D: E.78, A.164, R.165, F.168, N.169 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.168 Hydrogen bonds: D:N.169

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.4: 2 residues within 4Å: Chain A: D.322, D.376 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.322, H2O.1, H2O.1, H2O.3, H2O.7, H2O.9 MG.8: 1 residues within 4Å: Chain B: D.322 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.322, H2O.10, H2O.10, H2O.13, H2O.14, H2O.16 MG.9: 5 residues within 4Å: Chain B: G.305, S.306, D.320, D.322, D.324 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.322, B:D.324, H2O.10, H2O.15 MG.12: 1 residues within 4Å: Chain C: D.322 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:D.322, H2O.17, H2O.18, H2O.21, H2O.22, H2O.25 MG.16: 2 residues within 4Å: Chain D: D.322, D.376 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.322, H2O.26, H2O.26, H2O.31 MG.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuwabara, N. et al., Crystal structures of fukutin-related protein (FKRP), a ribitol-phosphate transferase related to muscular dystrophy. Nat Commun (2020)

Release Date

2020-01-15

Peptides

Fukutin-related protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Fukutin-related protein

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