SMTL ID : 1f06.3 (2 other biounits)

THREE DIMENSIONAL STRUCTURE OF THE TERNARY COMPLEX OF CORYNEBACTERIUM GLUTAMICUM DIAMINOPIMELATE DEHYDROGENASE NADPH-L-2-AMINO-6-METHYLENE-PIMELATE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

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

NDP.1: 21 residues within 4Å: Chain A: G.10, Y.11, G.12, N.13, L.14, S.35, R.36, R.37, C.65, M.66, G.67, S.68, T.88, D.90, T.117, G.118, W.119, D.120, P.121, N.270, T.274 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:T.274 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.65, A:M.66, A:S.68, A:T.88, A:T.88, A:W.119, A:D.120 Water bridges: A:Y.11, A:G.12, A:G.15, A:R.37 Salt bridges: A:R.36, A:R.37 pi-Cation interactions: A:R.37, A:R.37 NDP.2: 26 residues within 4Å: Chain B: G.10, Y.11, G.12, N.13, L.14, S.35, R.36, R.37, C.65, M.66, G.67, S.68, T.88, D.90, T.117, G.118, W.119, D.120, P.121, Q.150, G.151, D.154, R.157, N.270, T.274 Ligands: 2NP.3 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:T.274 Hydrogen bonds: B:Y.11, B:G.12, B:N.13, B:N.13, B:L.14, B:R.36, B:R.36, B:C.65, B:S.68, B:S.68, B:T.88, B:T.88, B:D.90, B:W.119, B:D.120, B:D.154 Water bridges: B:G.15, B:R.37, B:A.69, B:D.154, B:R.157, B:R.157 Salt bridges: B:R.36, B:R.37, B:R.157 pi-Cation interactions: B:R.37, B:R.37

1 x 2NP: L-2-AMINO-6-METHYLENE-PIMELIC ACID(Non-covalent)

2NP.3: 14 residues within 4Å: Chain B: D.90, W.119, D.120, W.144, L.148, S.149, Q.150, G.151, H.152, T.169, R.195, H.244, N.270 Ligands: NDP.2 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:D.90, B:W.119 Hydrogen bonds: B:W.144, B:S.149, B:Q.150, B:G.151, B:T.169, B:N.270, B:N.270 Water bridges: B:H.152 Salt bridges: B:H.152, B:R.195, B:H.244

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cirilli, M. et al., The three-dimensional structure of the ternary complex of Corynebacterium glutamicum diaminopimelate dehydrogenase-NADPH-L-2-amino-6-methylene-pimelate. Protein Sci. (2000)

Release Date

2001-05-14

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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