SMTL ID : 2qqc.1 (1 other biounit)

E109Q mutant of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannashii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

hetero-3-3-mer

Ligands

3 x AG2: AGMATINE(Non-covalent)

AG2.1: 13 residues within 4Å: Chain A: S.53 Chain B: X.1, I.2, I.55, M.56, Q.57, R.82 Chain C: L.32, F.35, D.36, L.39, G.45, V.47 6 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: C:L.32 Hydrogen bonds: C:G.45, A:S.53, B:Q.57, B:R.82 Salt bridges: C:D.36 AG2.2: 13 residues within 4Å: Chain A: L.32, F.35, D.36, L.39, G.45, V.47 Chain E: S.53 Chain F: X.1, I.2, I.55, M.56, Q.57, R.82 6 PLIP interactions: 3 interactions with chain A, 1 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: A:D.36 Hydrogen bonds: A:G.45, E:S.53, F:Q.57, F:R.82 Salt bridges: A:D.36 AG2.5: 12 residues within 4Å: Chain C: S.53 Chain D: X.1, I.2, I.55, Q.57, R.82 Chain E: L.32, F.35, D.36, L.39, G.45, V.47 7 PLIP interactions: 3 interactions with chain C, 3 interactions with chain E, 1 interactions with chain D Hydrogen bonds: C:S.53, E:G.45, D:R.82 Water bridges: C:S.53, C:S.53 Hydrophobic interactions: E:D.36 Salt bridges: E:D.36

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 5 residues within 4Å: Chain A: L.32, F.35 Chain B: Y.25, Y.27, I.29 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.32, A:F.35, B:Y.27, B:I.29 MPD.4: 4 residues within 4Å: Chain C: L.32, F.35 Chain D: Y.25, Y.27 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:Y.27 Hydrophobic interactions: C:L.32, C:F.35 MPD.6: 6 residues within 4Å: Chain C: S.53 Chain E: L.32, F.35 Chain F: Y.25, Y.27, I.29 3 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: F:I.29, E:F.35 Water bridges: C:S.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Soriano, E.V. et al., Structures of the N47A and E109Q mutant proteins of pyruvoyl-dependent arginine decarboxylase from Methanococcus jannaschii. Acta Crystallogr.,Sect.D (2008)

Release Date

2008-03-18

Peptides

Pyruvoyl-dependent arginine decarboxylase subunit beta: ACE
Pyruvoyl-dependent arginine decarboxylase subunit alpha: 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 subunit beta

Pyruvoyl-dependent arginine decarboxylase subunit alpha

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