SMTL ID : 6ia6.1

Crystal structure of the bacterial Dehalococcoides mccartyi Elp3 with desulfo-CoA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x DCA: DESULFO-COENZYME A(Non-covalent)

DCA.1: 20 residues within 4Å: Chain A: V.14, K.80, R.130, V.132, K.196, A.389, L.390, H.391, V.392, G.397, R.398, G.399, L.400, G.401, R.402, G.428, A.429, E.431, Y.432, Y.433 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:V.132, A:L.390, A:Y.432 Hydrogen bonds: A:K.80, A:R.130, A:V.392, A:G.397, A:G.399, A:G.401, A:R.402, A:G.428, A:Y.432, A:Y.432, A:Y.433 Salt bridges: A:R.402 pi-Stacking: A:Y.432, A:Y.432 DCA.4: 20 residues within 4Å: Chain B: V.14, K.80, R.130, V.132, K.196, A.389, L.390, H.391, V.392, G.397, R.398, G.399, L.400, G.401, R.402, G.428, A.429, E.431, Y.432, Y.433 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:V.132, B:L.390, B:Y.432 Hydrogen bonds: B:K.80, B:R.130, B:V.392, B:G.397, B:G.399, B:G.401, B:R.402, B:G.428, B:Y.432, B:Y.432, B:Y.433 Salt bridges: B:R.402 pi-Stacking: B:Y.432, B:Y.432

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.2: 9 residues within 4Å: Chain A: C.30, Y.32, C.33, R.176 Chain B: C.30, Y.32, C.33, R.176 Ligands: FES.5 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, Metal complexes: A:C.33, B:C.33 FES.5: 9 residues within 4Å: Chain A: C.30, Y.32, C.33, R.176 Chain B: C.30, Y.32, C.33, R.176 Ligands: FES.2 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, Metal complexes: A:C.33, B:C.33

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

PO4.3: 9 residues within 4Å: Chain A: R.158, K.196, H.198, D.229, R.277, I.316, L.363, R.365, A.389 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.198, A:R.365 PO4.6: 9 residues within 4Å: Chain B: R.158, K.196, H.198, D.229, R.277, I.316, L.363, R.365, A.389 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:H.198, B:R.365

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lin, T.Y. et al., The Elongator subunit Elp3 is a non-canonical tRNA acetyltransferase. Nat Commun (2019)

Release Date

2019-02-20

Peptides

ELP3 family, ELP3 family: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

ELP3 family, ELP3 family