SMTL ID : 3asv.1 (1 other biounit)

The Closed form of serine dehydrogenase complexed with NADP+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

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

NAP.1: 29 residues within 4Å: Chain A: G.7, T.9, A.10, G.11, F.12, G.31, R.32, R.33, L.53, D.54, V.55, R.56, N.81, A.82, G.83, T.105, I.132, G.133, S.134, Y.147, K.151, P.177, G.178, L.179, V.180, T.183, E.184, F.185 Ligands: PO4.2 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:F.12 Hydrogen bonds: A:G.7, A:T.9, A:T.9, A:A.10, A:F.12, A:R.32, A:R.33, A:R.33, A:D.54, A:V.55, A:R.56, A:A.82, A:G.83, A:K.151, A:V.180, A:V.180, A:T.183, A:E.184, A:F.185 Water bridges: A:G.13, A:R.32, A:R.32, A:Y.201 Salt bridges: A:R.32, A:R.33 pi-Stacking: A:F.185 pi-Cation interactions: A:R.32 NAP.3: 28 residues within 4Å: Chain B: G.7, T.9, A.10, G.11, F.12, R.32, R.33, L.53, D.54, V.55, R.56, N.81, A.82, G.83, T.105, I.132, G.133, S.134, Y.147, K.151, P.177, G.178, V.180, T.183, E.184, F.185, Y.201 Ligands: PO4.4 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:F.12, B:P.177 Hydrogen bonds: B:T.9, B:T.9, B:A.10, B:A.10, B:F.12, B:R.32, B:R.33, B:R.33, B:D.54, B:V.55, B:R.56, B:A.82, B:G.83, B:Y.147, B:K.151, B:V.180, B:V.180, B:T.183, B:E.184, B:F.185 Water bridges: B:T.105 Salt bridges: B:R.32, B:R.33 pi-Cation interactions: B:R.32 NAP.5: 29 residues within 4Å: Chain C: G.7, T.9, A.10, G.11, F.12, G.31, R.32, R.33, L.53, D.54, V.55, R.56, N.81, A.82, G.83, T.105, I.132, G.133, S.134, Y.147, K.151, P.177, G.178, L.179, V.180, T.183, E.184, F.185 Ligands: PO4.6 28 PLIP interactions: 28 interactions with chain C Hydrophobic interactions: C:F.12 Hydrogen bonds: C:G.7, C:T.9, C:T.9, C:A.10, C:F.12, C:R.32, C:R.33, C:R.33, C:D.54, C:V.55, C:R.56, C:A.82, C:G.83, C:K.151, C:V.180, C:V.180, C:T.183, C:E.184, C:F.185 Water bridges: C:G.13, C:R.32, C:R.32, C:Y.201 Salt bridges: C:R.32, C:R.33 pi-Stacking: C:F.185 pi-Cation interactions: C:R.32 NAP.7: 28 residues within 4Å: Chain D: G.7, T.9, A.10, G.11, F.12, R.32, R.33, L.53, D.54, V.55, R.56, N.81, A.82, G.83, T.105, I.132, G.133, S.134, Y.147, K.151, P.177, G.178, V.180, T.183, E.184, F.185, Y.201 Ligands: PO4.8 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:F.12, D:P.177 Hydrogen bonds: D:T.9, D:T.9, D:A.10, D:A.10, D:F.12, D:R.32, D:R.33, D:R.33, D:D.54, D:V.55, D:R.56, D:A.82, D:G.83, D:Y.147, D:K.151, D:V.180, D:V.180, D:T.183, D:E.184, D:F.185 Water bridges: D:T.105 Salt bridges: D:R.32, D:R.33 pi-Cation interactions: D:R.32

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 9 residues within 4Å: Chain A: S.134, T.135, A.136, Y.141, Y.147, G.178, F.185, R.189 Ligands: NAP.1 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.134, A:S.134, A:T.135, A:Y.147, A:R.189 Water bridges: A:V.180 PO4.4: 9 residues within 4Å: Chain B: S.134, A.136, Y.141, Y.147, P.177, G.178, F.185, R.189 Ligands: NAP.3 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.134, B:Y.141, B:R.189 PO4.6: 9 residues within 4Å: Chain C: S.134, T.135, A.136, Y.141, Y.147, G.178, F.185, R.189 Ligands: NAP.5 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:S.134, C:S.134, C:T.135, C:Y.147, C:R.189 Water bridges: C:V.180 PO4.8: 9 residues within 4Å: Chain D: S.134, A.136, Y.141, Y.147, P.177, G.178, F.185, R.189 Ligands: NAP.7 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.134, D:Y.141, D:R.189

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamazawa, R. et al., Crystal structure of serine dehydrogenase from Escherichia coli: important role of the C-terminal region for closed-complex formation. J.Biochem. (2011)

Release Date

2011-10-12

Peptides

Short-chain dehydrogenase/reductase SDR: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Short-chain dehydrogenase/reductase SDR

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