SMTL ID : 5dj3.1 (2 other biounits)

Structure of the PLP-Dependent L-Arginine Hydroxylase MppP with D-Arginine Bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.23 Å

Oligo State

homo-dimer

Ligands

2 x 5DK: (E)-N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-D-arginine(Non-covalent)

5DK.1: 19 residues within 4Å: Chain A: D.27, G.28, H.29, S.89, S.90, S.91, F.115, I.118, T.156, N.160, D.188, S.190, F.191, K.221, D.227, K.229, V.309, R.352 Chain B: L.252 25 PLIP interactions: 23 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.115, A:F.115, A:T.156, B:L.252 Hydrogen bonds: A:D.27, A:G.28, A:S.89, A:S.89, A:S.90, A:S.91, A:S.91, A:N.160, A:K.229, B:L.252 Water bridges: A:S.89, A:S.91, A:D.188, A:K.221 Salt bridges: A:D.27, A:H.29, A:K.221, A:D.227, A:K.229, A:R.352 pi-Cation interactions: A:K.221 5DK.2: 20 residues within 4Å: Chain A: Y.88, L.252 Chain B: D.27, G.28, H.29, S.89, S.90, S.91, F.115, I.118, T.156, N.160, D.188, S.190, F.191, K.221, D.227, K.229, V.309, R.352 26 PLIP interactions: 22 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:F.115, B:T.156, B:F.191 Hydrogen bonds: B:D.27, B:G.28, B:S.89, B:S.90, B:S.90, B:S.91, B:S.91, B:N.160, B:K.221, B:K.229 Water bridges: B:D.227, A:Y.88, A:Y.88, A:Y.88, A:Y.88 Salt bridges: B:D.27, B:H.29, B:K.221, B:D.227, B:K.229, B:R.352 pi-Cation interactions: B:H.29, B:K.221

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Han, L. et al., Streptomyces wadayamensis MppP Is a Pyridoxal 5'-Phosphate-Dependent l-Arginine alpha-Deaminase, gamma-Hydroxylase in the Enduracididine Biosynthetic Pathway. Biochemistry (2015)

Release Date

2015-11-25

Peptides

PLP-Dependent L-Arginine Hydroxylase MppP: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
C

PLP-Dependent L-Arginine Hydroxylase MppP

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