SMTL ID : 4x4w.1

Crystal structure of the full-length human mitochondrial CCA-adding enzyme

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

5 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: P.186, H.224, N.226, H.227 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.226, A:H.227 Salt bridges: A:H.224 SO4.4: 4 residues within 4Å: Chain A: R.368, S.373 Chain B: S.21, H.90 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.373 Salt bridges: A:R.368, B:H.90 SO4.12: 4 residues within 4Å: Chain B: P.186, H.224, N.226, H.227 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.226, B:H.227 Water bridges: B:H.224, B:H.224 Salt bridges: B:H.224 SO4.15: 5 residues within 4Å: Chain A: H.365, K.369 Chain B: R.73, R.88, E.91 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Salt bridges: B:R.73, B:R.88, A:K.369 SO4.16: 7 residues within 4Å: Chain A: H.365, R.368, K.369 Chain B: R.73, L.89, H.90, E.91 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Water bridges: A:R.368, B:R.73, B:R.73, B:E.91 Salt bridges: A:H.365, A:R.368, B:R.73, B:H.90 Hydrogen bonds: B:H.90

2 x FLC: CITRATE ANION(Non-covalent)

FLC.2: 8 residues within 4Å: Chain A: G.37, G.38, R.41, N.130, R.174, R.177, F.178, K.218 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.38 Water bridges: A:R.125 Salt bridges: A:R.41, A:R.174, A:R.174, A:R.177, A:R.177, A:K.218 FLC.13: 7 residues within 4Å: Chain B: G.38, R.41, N.130, R.174, R.177, F.178, K.218 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:G.38, B:R.174, B:R.174, B:R.177, B:R.177 Salt bridges: B:R.41, B:R.41, B:R.174, B:R.174, B:R.177, B:R.177

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: D.53, T.97, R.100, R.124, R.125, R.171 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.100, A:R.100, A:R.124, A:R.124 Water bridges: A:D.126 GOL.7: 3 residues within 4Å: Chain A: M.4, L.140, Y.147 3 PLIP interactions: 3 interactions with chain A Water bridges: A:L.140, A:Y.147, A:Y.147 GOL.8: 1 residues within 4Å: Chain A: F.2 No protein-ligand interaction detected (PLIP) GOL.14: 6 residues within 4Å: Chain B: D.53, T.97, R.100, R.124, R.125, D.126 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.53, B:R.100, B:R.100, B:R.124, B:R.124 Water bridges: B:R.125 GOL.18: 5 residues within 4Å: Chain A: S.374, G.375, K.376, E.377 Chain B: K.28 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.28, A:S.374, A:G.375 GOL.19: 6 residues within 4Å: Chain B: I.101, F.114, T.115, T.116, D.117, K.120 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.115, B:T.116, B:D.117 Water bridges: B:D.117, B:D.117

8 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 2 residues within 4Å: Chain A: A.290, K.291 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: I.207, S.208, R.211 Ligand excluded by PLIP CL.9: 2 residues within 4Å: Chain A: F.360, R.386 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: R.88, E.91 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: S.248, L.249, E.250 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain B: S.248, L.249, E.250 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain B: P.359, F.360, R.386 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain B: I.207, S.208, R.211 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuhn, C.D. et al., On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme. Cell (2015)

Release Date

2015-02-11

Peptides

CCA tRNA nucleotidyltransferase 1, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

CCA tRNA nucleotidyltransferase 1, mitochondrial