SMTL ID : 3wyc.1

Structure of a meso-diaminopimelate dehydrogenase in complex with NADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

homo-dimer

Ligands

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 23 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, D.94, V.121, G.122, W.123, D.124, P.125, N.276, T.280 Ligands: NES.2 29 PLIP interactions: 29 interactions with chain A Hydrophobic interactions: A:T.280 Hydrogen bonds: A:Y.11, A:N.13, A:N.13, A:L.14, A:R.36, A:R.36, A:R.37, A:C.69, A:S.72, A:S.92, A:W.123, A:D.124, A:P.125 Water bridges: A:V.9, A:G.12, A:G.15, A:R.16, A:R.16, A:F.34, A:R.36, A:R.36, A:A.73, A:D.94, A:D.94 Salt bridges: A:R.36, A:R.37 pi-Cation interactions: A:R.37, A:R.37 NAP.4: 23 residues within 4Å: Chain B: 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, D.94, V.121, G.122, W.123, D.124, P.125, N.276, T.280 Ligands: NES.5 32 PLIP interactions: 32 interactions with chain B Hydrophobic interactions: B:T.280 Hydrogen bonds: B:Y.11, B:N.13, B:N.13, B:L.14, B:T.35, B:R.36, B:R.36, B:R.37, B:C.69, B:S.72, B:S.92, B:W.123, B:D.124, B:P.125 Water bridges: B:V.9, B:G.12, B:G.15, B:R.16, B:R.16, B:R.16, B:F.34, B:R.36, B:R.36, B:A.73, B:D.94, B:D.94, B:D.94 Salt bridges: B:R.36, B:R.37 pi-Cation interactions: B:R.37, B:R.37

4 x NES: 2-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-ETHANESULFONIC ACID(Non-covalent)

NES.2: 10 residues within 4Å: Chain A: W.123, D.124, W.148, V.152, S.153, H.156, T.173, R.199, H.249 Ligands: NAP.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.94, A:D.124, A:V.152 Water bridges: A:Q.154 Salt bridges: A:H.156, A:R.199, A:H.249 NES.3: 7 residues within 4Å: Chain A: R.36, V.53, D.54, E.78, Q.79, Y.82, F.83 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.54, A:Q.79 NES.5: 11 residues within 4Å: Chain B: D.94, W.123, D.124, W.148, V.152, S.153, H.156, T.173, R.199, H.249 Ligands: NAP.4 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:D.94, B:D.94, B:D.124, B:V.152 Water bridges: B:Q.154, B:N.276 Salt bridges: B:H.156, B:R.199, B:H.249 NES.6: 7 residues within 4Å: Chain B: R.36, V.53, D.54, E.78, Q.79, Y.82, F.83 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.54, B:D.54, B:Q.79

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Akita, H. et al., Structural insight into the thermostable NADP(+)-dependent meso-diaminopimelate dehydrogenase from Ureibacillus thermosphaericus. Acta Crystallogr.,Sect.D (2015)

Release Date

2015-05-06

Peptides

Meso-diaminopimelate D-dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Meso-diaminopimelate D-dehydrogenase

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