SMTL ID : 5ks8.1

Crystal structure of two-subunit pyruvate carboxylase from Methylobacillus flagellatus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.01 Å

Oligo State

hetero-2-4-mer

Ligands

1 x BTI: 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL(Covalent)

BTI.1: 16 residues within 4Å: Chain C: K.581 Chain D: Q.16, A.49, D.52, R.56, Y.57, R.83, Y.90, G.299, M.300, N.303, Q.307, T.338, S.341, Q.342 Ligands: PYR.4 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:Q.342 Hydrogen bonds: D:T.338, D:S.341, D:Q.342, D:Q.342

2 x PYR: PYRUVIC ACID(Non-covalent)

PYR.2: 10 residues within 4Å: Chain C: R.12, Q.16, G.48, A.49, L.81, R.83, F.116, K.174, M.176 Ligands: MN.3 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.12, C:Q.16, C:A.49, C:K.174 Salt bridges: C:R.12, C:R.83 PYR.4: 11 residues within 4Å: Chain D: R.12, Q.16, G.48, A.49, L.81, R.83, F.116, K.174, T.338 Ligands: BTI.1, MN.5 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:R.12, D:R.12, D:Q.16, D:Q.16, D:A.49, D:K.174 Salt bridges: D:R.12, D:R.83

3 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 7 residues within 4Å: Chain C: R.12, D.13, K.174, M.176, H.203, H.205 Ligands: PYR.2 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.13, C:H.203, C:H.205 MN.5: 6 residues within 4Å: Chain D: R.12, D.13, K.174, H.203, H.205 Ligands: PYR.4 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.13, D:H.203, D:H.205 MN.6: 6 residues within 4Å: Chain F: R.12, D.13, K.174, M.176, H.203, H.205 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.13, F:H.205

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Choi, P.H. et al., A distinct holoenzyme organization for two-subunit pyruvate carboxylase. Nat Commun (2016)

Release Date

2016-10-19

Peptides

Pyruvate carboxylase subunit alpha: AB
Pyruvate carboxylase subunit beta: CDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Pyruvate carboxylase subunit alpha

Pyruvate carboxylase subunit beta