SMTL ID : 3rc9.1

Crystal Structure of the K102A mutant of KijD10, a 3-ketoreductase from Actinomadura kijaniata in complex with TDP-benzene and NADP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

monomer

Ligands

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

NAP.1: 21 residues within 4Å: Chain A: G.34, C.35, A.36, D.37, I.38, S.60, R.61, R.65, Y.81, P.96, L.97, P.98, A.99, L.101, H.102, E.119, A.120, P.121, V.193, D.200 Ligands: TLO.5 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:C.35, A:D.37, A:R.61, A:R.61, A:R.65, A:Y.81, A:Y.81, A:H.102, A:D.200 Water bridges: A:R.61, A:A.99, A:E.119 Salt bridges: A:R.61 pi-Cation interactions: A:R.61, A:R.61

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

CL.2: 2 residues within 4Å: Chain A: N.274, H.288 Ligand excluded by PLIP

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain A: R.341, T.342, A.344, D.346 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.342

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

PO4.4: 2 residues within 4Å: Chain A: H.303, K.308 3 PLIP interactions: 3 interactions with chain A Water bridges: A:K.308 Salt bridges: A:H.303, A:K.308

2 x TLO: 5'-O-[(S)-hydroxy{[(S)-hydroxy(phenoxy)phosphoryl]oxy}phosphoryl]thymidine(Non-covalent)

TLO.5: 11 residues within 4Å: Chain A: I.38, R.41, R.42, F.177, I.179, P.180, Y.204, Y.258, R.275, T.278 Ligands: NAP.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.38, A:F.177, A:F.177, A:Y.204, A:Y.258, A:T.278 Hydrogen bonds: A:R.42, A:Y.258, A:N.260, A:T.278, A:T.278 Salt bridges: A:R.41, A:R.42 pi-Stacking: A:Y.258 TLO.6: 12 residues within 4Å: Chain A: M.144, L.150, H.151, H.155, R.156, A.159, R.207, L.211, F.212, E.325, W.326, D.329 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:A.159, A:L.211, A:F.212, A:E.325 Hydrogen bonds: A:R.207 Water bridges: A:E.145, A:H.151, A:R.156, A:R.207 Salt bridges: A:R.156 pi-Stacking: A:W.326

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kubiak, R.L. et al., Combined Structural and Functional Investigation of a C-3''-Ketoreductase Involved in the Biosynthesis of dTDP-l-Digitoxose. Biochemistry (2011)

Release Date

2011-06-08

Peptides

Sugar 3-ketoreductase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Sugar 3-ketoreductase