SMTL ID : 6kam.1

Crystal structure of FKRP in complex with Ba ion, CDP-ribtol, and sugar acceptor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.46 Å

Oligo State

homo-tetramer

Ligands

1 x MAN- NAG- NGA: 2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose

MAN-NAG-NGA.1: 8 residues within 4Å: Chain C: R.255, T.259, V.358, R.364, H.372 Chain D: H.212 Ligands: PO4.19, PO4.26 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:H.212, D:K.216, C:R.255, C:T.259

4 x ZN: ZINC ION(Non-covalent)

ZN.2: 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.8: 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.13: 4 residues within 4Å: Chain C: C.249, C.256, 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.20: 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.3: 5 residues within 4Å: Chain A: N.132, R.141, Y.142, G.143 Chain C: R.396 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:Q.442, A:N.132 NAG.4: 6 residues within 4Å: Chain A: E.78, R.165, F.168, N.169 Chain D: D.28, Q.32 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.168 Hydrogen bonds: A:N.169 NAG.9: 4 residues within 4Å: Chain B: N.132, R.141, Y.142, G.143 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.132 NAG.14: 5 residues within 4Å: Chain A: R.396, F.433 Chain C: N.132, R.141, Y.142 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.132 NAG.15: 6 residues within 4Å: Chain B: D.28, Q.32 Chain C: E.78, R.165, F.168, N.169 6 PLIP interactions: 3 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:E.78, C:F.168 Hydrogen bonds: C:N.169, B:D.28, B:Q.32, B:Q.32 NAG.21: 2 residues within 4Å: Chain D: N.132, R.141 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.132 NAG.22: 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

4 x CDP: CYTIDINE-5'-DIPHOSPHATE(Non-covalent)

CDP.5: 21 residues within 4Å: Chain A: D.263, G.304, G.305, L.308, R.312, I.317, W.319, D.320, Y.321, D.322, D.324, H.395, Q.397, V.437, N.440, P.441, Q.442, Y.443, P.444 Ligands: RB0.6, BA.7 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:G.305, A:R.312, A:R.312, A:D.320, A:D.322, A:Q.397, A:N.440, A:Q.442, A:Y.443 Salt bridges: A:H.395, A:H.395 CDP.10: 21 residues within 4Å: Chain B: G.304, G.305, L.308, R.312, I.317, W.319, D.320, Y.321, D.322, D.324, H.395, Q.397, F.433, V.437, N.440, P.441, Q.442, Y.443, P.444 Ligands: RB0.11, BA.12 10 PLIP interactions: 10 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 Water bridges: B:D.322 Salt bridges: B:H.395 CDP.16: 21 residues within 4Å: Chain C: G.304, G.305, L.308, R.312, I.317, W.319, D.320, Y.321, D.322, D.324, W.378, H.395, Q.397, V.437, N.440, P.441, Q.442, Y.443, P.444 Ligands: RB0.17, BA.18 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:G.305, C:R.312, C:R.312, C:D.320, C:D.322, C:D.324, C:Q.397, C:N.440, C:Q.442, C:Y.443 Salt bridges: C:H.395, C:H.395 CDP.23: 18 residues within 4Å: Chain D: G.305, L.308, R.312, I.317, W.319, D.320, D.322, D.324, H.395, Q.397, V.437, N.440, P.441, Q.442, Y.443, P.444 Ligands: RB0.24, BA.25 13 PLIP interactions: 13 interactions with chain D Hydrophobic interactions: D:V.437 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 Water bridges: D:D.322, D:D.324 Salt bridges: D:H.395, D:H.395

4 x RB0: D-ribitol(Non-covalent)

RB0.6: 8 residues within 4Å: Chain A: E.303, G.304, D.324, W.378, H.395, Q.397, D.398 Ligands: CDP.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.395, A:D.398, A:V.399 RB0.11: 11 residues within 4Å: Chain B: E.303, G.304, D.324, W.378, F.380, L.393, H.395, Q.397, D.398, K.432 Ligands: CDP.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.303, B:Q.397, B:K.432, B:K.432 RB0.17: 11 residues within 4Å: Chain C: E.303, G.304, D.324, W.378, F.380, K.389, L.393, H.395, Q.397, D.398 Ligands: CDP.16 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:W.378 Hydrogen bonds: C:W.378, C:K.389, C:H.395, C:Q.397, C:D.398 RB0.24: 9 residues within 4Å: Chain D: E.303, G.304, D.324, W.378, F.380, H.395, Q.397, D.398 Ligands: CDP.23 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:W.378 Hydrogen bonds: D:H.395, D:Q.397, D:D.398

4 x BA: BARIUM ION(Non-covalent)

BA.7: 4 residues within 4Å: Chain A: D.320, D.322, D.324 Ligands: CDP.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.320, A:D.322 BA.12: 4 residues within 4Å: Chain B: D.320, D.322, D.324 Ligands: CDP.10 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.322, B:D.324 BA.18: 4 residues within 4Å: Chain C: D.320, D.322, D.324 Ligands: CDP.16 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.322, C:D.324 BA.25: 4 residues within 4Å: Chain D: D.320, D.322, D.324 Ligands: CDP.23 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.322, D:D.324

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.19: 5 residues within 4Å: Chain C: R.255, T.259, V.260, H.374 Ligands: MAN-NAG-NGA.1 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.260 Salt bridges: C:R.255, C:H.374 PO4.26: 3 residues within 4Å: Chain D: H.212, K.216 Ligands: MAN-NAG-NGA.1 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:H.212, D:K.216

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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