SMTL ID : 6ujd.1

Crystal structure of Cysteine-tRNA ligase from Elizabethkingia sp.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: C.37, C.233, H.258, E.262 Ligands: CL.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.37, A:C.233, A:H.258 ZN.8: 5 residues within 4Å: Chain B: C.37, C.233, H.258, E.262 Ligands: CL.11 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.37, B:C.233, B:H.258

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

CL.2: 3 residues within 4Å: Chain A: F.204, A.205, K.208 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: R.51, S.55, F.325, A.328 Ligand excluded by PLIP CL.4: 8 residues within 4Å: Chain A: C.37, G.38, N.75, T.77, W.229, C.233, H.258 Ligands: ZN.1 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: F.204, A.205, K.208 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain B: R.51, S.55, F.325, A.328 Ligand excluded by PLIP CL.11: 8 residues within 4Å: Chain B: C.37, G.38, N.75, T.77, W.229, C.233, H.258 Ligands: ZN.8 Ligand excluded by PLIP

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

PO4.5: 6 residues within 4Å: Chain A: K.21, H.329, R.331, D.384, D.385, N.387 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.384 Salt bridges: A:K.21, A:H.329, A:R.331 PO4.12: 6 residues within 4Å: Chain B: K.21, H.329, R.331, D.384, D.385, N.387 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.384 Salt bridges: B:K.21, B:H.329, B:R.331

2 x PG5: 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE(Non-covalent)

PG5.6: 3 residues within 4Å: Chain A: L.82, Q.213, I.215 No protein-ligand interaction detected (PLIP) PG5.13: 3 residues within 4Å: Chain B: L.82, Q.213, I.215 No protein-ligand interaction detected (PLIP)

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 3 residues within 4Å: Chain A: I.66, G.67, Y.68 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.67 EDO.14: 3 residues within 4Å: Chain B: I.66, G.67, Y.68 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.67 Water bridges: B:Y.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal structure of Cysteine-tRNA ligase from Elizabethkingia sp. TO BE PUBLISHED

Release Date

2019-10-16

Peptides

Cysteine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cysteine--tRNA ligase