SMTL ID : 5gz6.1

Structure of D-amino acid dehydrogenase in complex with NADPH and 2-keto-6-aminocapronic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.74 Å

Oligo State

homo-dimer

Ligands

1 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 22 residues within 4Å: Chain A: G.10, Y.11, G.12, N.13, L.14, T.35, R.36, R.37, C.69, G.70, G.71, S.72, D.75, S.92, A.94, V.121, G.122, W.123, D.124, P.125, T.280 Ligands: 7C3.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:T.280 Hydrogen bonds: A:Y.11, A:N.13, A:N.13, A:L.14, A:T.35, A:R.36, A:R.37, A:C.69, A:S.72, A:W.123, A:D.124, A:P.125 Water bridges: A:G.12, A:G.15, A:R.37, A:A.73, A:Q.79, A:S.92 pi-Cation interactions: A:R.37

1 x 7C3: 6-azanyl-2-oxidanylidene-hexanoic acid(Non-covalent)

7C3.2: 5 residues within 4Å: Chain A: W.123, D.124, W.148, K.150 Ligands: NDP.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.123, A:D.124, A:K.150 Hydrogen bonds: A:W.148, A:K.150 Salt bridges: A:K.150

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

SO4.3: 6 residues within 4Å: Chain A: N.249, L.273, N.276, P.277, M.278, F.279 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.249, A:N.276, A:M.278, A:F.279 Water bridges: A:T.280 SO4.5: 3 residues within 4Å: Chain B: G.12, N.13, R.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.13 Salt bridges: B:R.16

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 6 residues within 4Å: Chain A: L.127, L.130, N.131 Chain B: L.127, N.131, F.310 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.310, A:L.130 Hydrogen bonds: B:N.131, A:N.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hayashi, J. et al., Structure-Based Engineering of an Artificially Generated NADP+-Dependent d-Amino Acid Dehydrogenase. Appl. Environ. Microbiol. (2017)

Release Date

2017-04-12

Peptides

Meso-diaminopimelate D-dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Meso-diaminopimelate D-dehydrogenase

Related Entries With Identical Sequence