SMTL ID : 3mbh.1

Crystal structure of a putative phosphomethylpyrimidine kinase (BT_4458) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.00 A resolution (orthorhombic form with pyridoxal)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-hexamer

Ligands

6 x PXL: 3-HYDROXY-5-(HYDROXYMETHYL)-2-METHYLISONICOTINALDEHYDE(Non-covalent)

PXL.1: 11 residues within 4Å: Chain A: D.15, S.17, V.22, L.46, H.49, T.50, Q.51, Y.85, V.114, Y.122, D.225 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.22, A:L.46, A:Y.85 Hydrogen bonds: A:S.23, A:T.50, A:Q.51 Water bridges: A:Y.85, A:G.222, A:G.222, A:D.225 PXL.3: 12 residues within 4Å: Chain B: D.15, S.17, V.22, S.23, L.46, H.49, T.50, Q.51, Y.85, V.114, Y.122, D.225 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:V.22, B:L.46, B:Y.85 Hydrogen bonds: B:T.50, B:Q.51 Water bridges: B:Y.85, B:G.222, B:G.222, B:D.225 PXL.4: 12 residues within 4Å: Chain C: D.15, S.17, V.22, S.23, L.46, H.49, T.50, Q.51, Y.85, V.114, Y.122, D.225 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:V.22, C:L.46, C:Y.85, C:Y.85 Hydrogen bonds: C:S.23, C:T.50, C:Q.51 Water bridges: C:G.222, C:G.222, C:D.225 PXL.6: 12 residues within 4Å: Chain D: D.15, S.17, V.22, S.23, L.46, H.49, T.50, Q.51, Y.85, V.114, Y.122, D.225 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:L.46, D:Y.85 Hydrogen bonds: D:S.23, D:T.50, D:Q.51 Water bridges: D:Y.85, D:G.222, D:G.222, D:G.222, D:D.225 PXL.7: 12 residues within 4Å: Chain E: D.15, S.17, V.22, S.23, L.46, H.49, T.50, Q.51, Y.85, V.114, Y.122, D.225 12 PLIP interactions: 12 interactions with chain E Hydrophobic interactions: E:V.22, E:L.46, E:Y.85, E:Y.85 Hydrogen bonds: E:S.23, E:T.50, E:Q.51 Water bridges: E:Y.122, E:G.222, E:G.222, E:G.222, E:D.225 PXL.9: 11 residues within 4Å: Chain F: D.15, S.17, V.22, L.46, H.49, T.50, Q.51, Y.85, V.114, Y.122, D.225 10 PLIP interactions: 10 interactions with chain F Hydrophobic interactions: F:L.46, F:Y.85, F:Y.85 Hydrogen bonds: F:S.23, F:T.50, F:Q.51 Water bridges: F:Y.85, F:D.225, F:D.225, F:D.225

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

CL.2: 3 residues within 4Å: Chain A: N.202, W.209, L.241 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain C: N.202, W.209, L.241 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain E: N.202, W.209, L.241, P.242 Ligand excluded by PLIP CL.10: 5 residues within 4Å: Chain C: F.260 Chain F: N.202, W.209, L.241, P.242 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of a putative phosphomethylpyrimidine kinase (BT_4458) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.00 A resolution (orthorhombic form with pyridoxal). To be Published

Release Date

2010-06-02

Peptides

Putative phosphomethylpyrimidine kinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Putative phosphomethylpyrimidine kinase

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