SMTL ID : 6n2a.1

Meso-Diaminopimelate Decarboxylase from Arabidopsis thaliana (Isoform 1)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PLP.1: 15 residues within 4Å: Chain A: A.61, K.63, N.105, R.151, H.202, S.205, G.241, G.242, E.278, P.279, G.280, R.281, Y.378 Chain B: C.349 Ligands: LYS.2 13 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: A:H.202, K.2 Hydrogen bonds: A:K.63, A:G.241, A:G.242, A:G.280, A:R.281, A:Y.378 Water bridges: A:N.105, A:T.206, B:C.349 pi-Stacking: A:H.202 Salt bridges: K.2 PLP.3: 15 residues within 4Å: Chain A: C.349 Chain B: A.61, K.63, N.105, R.151, H.202, S.205, G.241, G.242, E.278, P.279, G.280, R.281, Y.378 Ligands: LYS.4 13 PLIP interactions: 10 interactions with chain B, 2 Ligand-Ligand interactions, 1 interactions with chain A Hydrophobic interactions: B:H.202, K.4 Hydrogen bonds: B:K.63, B:G.241, B:G.242, B:G.280, B:R.281, B:Y.378 Water bridges: B:T.206, B:S.282, A:C.349 pi-Stacking: B:H.202 Salt bridges: K.4

2 x LYS: LYSINE(Non-covalent)

LYS.2: 11 residues within 4Å: Chain A: K.63, H.202, R.281, R.317, Y.321, Y.378, M.382 Chain B: C.349, E.350, Y.386 Ligands: PLP.1 9 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: A:Y.378, B:E.350 Hydrogen bonds: A:K.63, A:Y.321, B:E.350, K.2, K.2 Salt bridges: A:R.281, A:R.317 LYS.4: 10 residues within 4Å: Chain A: C.349, E.350, Y.386 Chain B: K.63, R.281, R.317, Y.321, Y.378, M.382 Ligands: PLP.3 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B, Hydrophobic interactions: A:E.350, B:Y.378, B:Y.378 Hydrogen bonds: A:E.350, B:K.63 Salt bridges: B:R.281, B:R.317

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Crowther, J.M. et al., Active site gating provides stereochemical control for meso-diaminopimelate decarboxylase. To Be Published

Release Date

2019-04-24

Peptides

Diaminopimelate decarboxylase 1, chloroplastic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Diaminopimelate decarboxylase 1, chloroplastic