SMTL ID : 6kal.1

Crystal structure of FKRP in complex with Mg ion and CMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.249, C.256, P.275, 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.6: 5 residues within 4Å: Chain B: C.249, C.256, P.275, 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.12: 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.18: 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)(Non-covalent)

NAG.2: 4 residues within 4Å: Chain A: N.132, R.141, Y.142, G.143 No protein-ligand interaction detected (PLIP) NAG.7: 2 residues within 4Å: Chain B: N.132, R.141 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.132 NAG.8: 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.13: 5 residues within 4Å: Chain A: F.433 Chain C: N.132, R.141, Y.142, G.143 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:F.433, C:N.132 NAG.14: 5 residues within 4Å: Chain A: L.451 Chain B: P.54, R.55 Chain C: N.169 Chain D: P.71 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:N.169, B:R.55 NAG.19: 5 residues within 4Å: Chain D: N.132, R.141, Y.142, G.143, E.240 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.132 NAG.20: 5 residues within 4Å: Chain D: E.78, A.164, R.165, F.168, N.169 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.168 Hydrogen bonds: D:N.169 Water bridges: D:N.169

4 x C5P: CYTIDINE-5'-MONOPHOSPHATE(Non-covalent)(Covalent)

C5P.3: 14 residues within 4Å: Chain A: G.304, G.305, L.308, R.312, I.317, W.319, D.320, D.322, D.324, Q.397, V.437, N.440, Q.442 Ligands: MG.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:G.305, A:R.312, A:R.312, A:D.320, A:N.440, A:Q.442, A:Q.442 Water bridges: A:D.322, A:D.324 C5P.9: 18 residues within 4Å: Chain B: G.304, G.305, L.308, R.312, I.317, W.319, D.320, D.322, D.324, Q.397, F.433, V.437, N.440, P.441, Q.442, Y.443, P.444 Ligands: MG.10 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.305, B:R.312, B:R.312, B:D.320, B:Q.397, B:N.440, B:Q.442, B:Y.443 C5P.15: 11 residues within 4Å: Chain C: G.305, L.308, R.312, I.317, W.319, D.320, V.437, N.440, P.441, Q.442 Ligands: MG.16 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:L.308, C:Q.442 Hydrogen bonds: C:G.305, C:R.312, C:R.312, C:D.324, C:N.440, C:Q.442 C5P.21: 16 residues within 4Å: Chain D: G.304, G.305, L.308, R.312, I.317, W.319, D.320, D.324, Q.397, V.437, N.440, P.441, Q.442, Y.443, P.444 Ligands: MG.22 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:G.305, D:R.312, D:R.312, D:D.320, D:Q.397, D:N.440, D:Q.442, D:Y.443

8 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: D.320, D.322, D.324 Ligands: C5P.3 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.322, A:D.324, C5P.3 MG.5: 3 residues within 4Å: Chain A: D.322, D.324, D.376 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.322, A:D.376, H2O.1 MG.10: 4 residues within 4Å: Chain B: D.320, D.322, D.324 Ligands: C5P.9 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:D.322, B:D.324, C5P.9 MG.11: 3 residues within 4Å: Chain B: D.322, D.324, D.376 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.322, B:D.324, B:D.376 MG.16: 4 residues within 4Å: Chain C: D.320, D.322, D.324 Ligands: C5P.15 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.322, C:D.324, H2O.6 MG.17: 4 residues within 4Å: Chain C: D.322, D.324, H.374, D.376 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.322, C:D.376, H2O.6 MG.22: 4 residues within 4Å: Chain D: D.320, D.322, D.324 Ligands: C5P.21 4 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: D:D.322, D:D.324, H2O.8, C5P.21 MG.23: 4 residues within 4Å: Chain D: D.322, D.324, D.376, W.378 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.322, D:D.324, D:D.376, H2O.8

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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