SMTL ID : 1n13.1 (1 other biounit)

The Crystal Structure of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannashii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

hetero-3-3-mer

Ligands

3 x AG2: AGMATINE(Non-covalent)

AG2.1: 11 residues within 4Å: Chain A: S.52 Chain B: X.1, I.55, E.57, R.82 Chain C: L.31, F.34, D.35, L.38, G.44, V.46 6 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: C:D.35 Hydrogen bonds: C:G.44, A:S.52, B:E.57, B:R.82 Salt bridges: C:D.35 AG2.3: 12 residues within 4Å: Chain C: S.52 Chain D: X.1, L.54, I.55, E.57, R.82 Chain E: L.31, F.34, D.35, L.38, G.44, V.46 9 PLIP interactions: 3 interactions with chain D, 3 interactions with chain E, 3 interactions with chain C Hydrophobic interactions: D:L.54, E:D.35 Hydrogen bonds: D:E.57, D:R.82, E:G.44, C:S.52 Salt bridges: E:D.35 Water bridges: C:S.52, C:S.52 AG2.6: 13 residues within 4Å: Chain A: L.31, F.34, D.35, L.38, G.44, V.46 Chain E: S.52 Chain F: X.1, I.2, I.55, M.56, E.57, R.82 8 PLIP interactions: 2 interactions with chain F, 4 interactions with chain A, 2 interactions with chain E Hydrogen bonds: F:E.57, F:R.82, A:G.44, E:S.52 Hydrophobic interactions: A:L.31, A:D.35 Salt bridges: A:D.35 Water bridges: E:S.52

4 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.2: 6 residues within 4Å: Chain A: P.30, L.31, F.34 Chain B: Y.25, Y.27, I.29 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.27, B:I.29, A:F.34, A:F.34 MRD.4: 5 residues within 4Å: Chain C: L.31, F.34 Chain D: Y.25, Y.27, I.29 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:F.34, C:F.34, D:I.29 Hydrogen bonds: D:Y.27 MRD.5: 6 residues within 4Å: Chain D: K.76, F.79, E.80, G.83, W.84, E.85 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:E.80 Hydrogen bonds: D:W.84 MRD.7: 6 residues within 4Å: Chain E: P.30, L.31, F.34 Chain F: Y.25, Y.27, I.29 4 PLIP interactions: 2 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:Y.27, F:I.29, E:F.34, E:F.34

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tolbert, W.D. et al., Pyruvoyl-Dependent Arginine Decarboxylase from Methanococcus jannaschii: Crystal Structures of the Self-Cleaved and S53A Proenzyme Forms. Structure (2003)

Release Date

2003-03-25

Peptides

Pyruvoyl-dependent arginine decarboxylase beta chain: ACE
Pyruvoyl-dependent arginine decarboxylase alpha chain: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

B
B

D
D

F
F

Pyruvoyl-dependent arginine decarboxylase beta chain

Pyruvoyl-dependent arginine decarboxylase alpha chain

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