SMTL ID : 7ea4.1 (1 other biounit)

Crystal Structure of L182E D-Succinylase (DSA) from Cupriavidus sp. P4-10-C

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

2 x CAD: CACODYLIC ACID(Non-covalent)

CAD.1: 6 residues within 4Å: Chain A: H.307, G.308, R.713, H.714, P.715 Ligands: SIN.6 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.247 CAD.4: 6 residues within 4Å: Chain A: T.220, L.221, P.222, E.223, N.484, Y.497 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.223, A:Y.497 Water bridges: A:T.220, A:T.220, A:D.486

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: H.304, S.543, R.547, A.739, N.744, S.746, A.756 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.543, A:R.547, A:N.744, A:S.746, A:S.746 GOL.3: 5 residues within 4Å: Chain A: H.179, G.181, T.183, Y.239, T.243 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.239, A:T.243, A:T.243 Water bridges: A:G.181, A:E.182, A:E.182

2 x SIN: SUCCINIC ACID(Non-covalent)

SIN.5: 11 residues within 4Å: Chain A: S.282, P.303, H.304, R.305, R.313, L.348, T.349, R.350, Y.433, E.460, N.523 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.348, A:R.350 Hydrogen bonds: A:S.282, A:H.304, A:R.350, A:Y.433, A:E.460, A:N.523 Salt bridges: A:R.305, A:R.313 SIN.6: 7 residues within 4Å: Chain A: Q.83, H.307, G.308, A.309, P.310, P.715 Ligands: CAD.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.83 Water bridges: A:A.309

1 x CO3: CARBONATE ION(Non-functional Binders)

CO3.7: 1 residues within 4Å: Chain A: R.773 No protein-ligand interaction detected (PLIP)

1 x CA: CALCIUM ION(Non-covalent)

CA.8: 6 residues within 4Å: Chain A: N.185, E.189, D.354, E.356, D.357, G.487 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:E.189, A:D.354, A:E.356, A:D.357, A:G.487

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

CL.9: 5 residues within 4Å: Chain A: W.485, D.486, G.487, L.488, F.489 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sumida, Y. et al., Protein Engineering of d-Succinylase from Cupriavidus sp. for d-Amino Acid Synthesis and the Structural Implications. Adv.Synth.Catal. (2021)

Release Date

2022-01-26

Peptides

D-succinylase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D-succinylase

Related Entries With Identical Sequence