SMTL ID : 3mbj.1

Crystal structure of a putative phosphomethylpyrimidine kinase (BT_4458) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.10 A resolution (rhombohedral form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

18 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.1: 5 residues within 4Å: Chain A: H.277, D.280 Chain F: H.277, D.280 Ligands: ZN.56 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain F Metal complexes: A:H.277, A:D.280, F:H.277, F:D.280 ZN.2: 1 residues within 4Å: Chain A: D.97 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.97, A:D.97 ZN.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.12: 5 residues within 4Å: Chain B: H.277, D.280 Chain E: H.277, D.280 Ligands: ZN.45 4 PLIP interactions: 2 interactions with chain E, 2 interactions with chain B Metal complexes: E:H.277, E:D.280, B:H.277, B:D.280 ZN.13: 1 residues within 4Å: Chain B: D.97 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.97, B:D.97 ZN.14: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.23: 5 residues within 4Å: Chain C: H.277, D.280 Chain D: H.277, D.280 Ligands: ZN.34 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain C Metal complexes: D:H.277, D:D.280, C:H.277, C:D.280 ZN.24: 1 residues within 4Å: Chain C: D.97 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.97, C:D.97 ZN.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.34: 5 residues within 4Å: Chain C: H.277, D.280 Chain D: H.277, D.280 Ligands: ZN.23 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Metal complexes: C:H.277, C:D.280, D:H.277, D:D.280 ZN.35: 1 residues within 4Å: Chain D: D.97 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.97, D:D.97 ZN.36: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.45: 5 residues within 4Å: Chain B: H.277, D.280 Chain E: H.277, D.280 Ligands: ZN.12 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain E Metal complexes: B:H.277, B:D.280, E:H.277, E:D.280 ZN.46: 1 residues within 4Å: Chain E: D.97 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.97, E:D.97 ZN.47: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ZN.56: 5 residues within 4Å: Chain A: H.277, D.280 Chain F: H.277, D.280 Ligands: ZN.1 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain F Metal complexes: A:H.277, A:D.280, F:H.277, F:D.280 ZN.57: 1 residues within 4Å: Chain F: D.97 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.97, F:D.97 ZN.58: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

CL.4: 3 residues within 4Å: Chain A: Y.3, A.4, K.6 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain B: Y.3, A.4, K.6 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain C: Y.3, A.4, K.6 Ligand excluded by PLIP CL.37: 3 residues within 4Å: Chain D: Y.3, A.4, K.6 Ligand excluded by PLIP CL.48: 3 residues within 4Å: Chain E: Y.3, A.4, K.6 Ligand excluded by PLIP CL.59: 3 residues within 4Å: Chain F: Y.3, A.4, K.6 Ligand excluded by PLIP

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 6 residues within 4Å: Chain A: H.219, Y.220, P.221, G.222, T.223, G.224 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.222, A:T.223, A:G.224 Water bridges: A:D.225 Salt bridges: A:H.219 SO4.6: 4 residues within 4Å: Chain A: I.99, K.100, R.103, K.139 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.103, A:K.139 SO4.16: 6 residues within 4Å: Chain B: H.219, Y.220, P.221, G.222, T.223, G.224 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.222, B:T.223, B:G.224 Water bridges: B:D.225 Salt bridges: B:H.219 SO4.17: 4 residues within 4Å: Chain B: I.99, K.100, R.103, K.139 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.103, B:K.139 SO4.27: 6 residues within 4Å: Chain C: H.219, Y.220, P.221, G.222, T.223, G.224 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.222, C:T.223, C:G.224 Water bridges: C:D.225 Salt bridges: C:H.219 SO4.28: 4 residues within 4Å: Chain C: I.99, K.100, R.103, K.139 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.103, C:K.139 SO4.38: 6 residues within 4Å: Chain D: H.219, Y.220, P.221, G.222, T.223, G.224 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:G.222, D:T.223, D:T.223, D:G.224 Water bridges: D:D.225 Salt bridges: D:H.219 SO4.39: 4 residues within 4Å: Chain D: I.99, K.100, R.103, K.139 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:R.103, D:K.139 SO4.49: 6 residues within 4Å: Chain E: H.219, Y.220, P.221, G.222, T.223, G.224 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:G.222, E:T.223, E:T.223, E:G.224 Water bridges: E:D.225 Salt bridges: E:H.219 SO4.50: 4 residues within 4Å: Chain E: I.99, K.100, R.103, K.139 2 PLIP interactions: 2 interactions with chain E Salt bridges: E:R.103, E:K.139 SO4.60: 6 residues within 4Å: Chain F: H.219, Y.220, P.221, G.222, T.223, G.224 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:G.222, F:T.223, F:T.223, F:G.224 Water bridges: F:D.225 Salt bridges: F:H.219 SO4.61: 4 residues within 4Å: Chain F: I.99, K.100, R.103, K.139 2 PLIP interactions: 2 interactions with chain F Salt bridges: F:R.103, F:K.139

6 x IMD: IMIDAZOLE(Non-covalent)

IMD.7: 4 residues within 4Å: Chain A: I.92, S.96, E.132, H.135 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.96, A:H.135 IMD.18: 4 residues within 4Å: Chain B: I.92, S.96, E.132, H.135 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.96, B:H.135 IMD.29: 4 residues within 4Å: Chain C: I.92, S.96, E.132, H.135 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.96, C:H.135 IMD.40: 4 residues within 4Å: Chain D: I.92, S.96, E.132, H.135 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:S.96 IMD.51: 4 residues within 4Å: Chain E: I.92, S.96, E.132, H.135 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:S.96 IMD.62: 4 residues within 4Å: Chain F: I.92, S.96, E.132, H.135 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:S.96

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

MPD.8: 6 residues within 4Å: Chain A: E.75, V.76, Q.77, D.101, F.102, Q.104 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Q.77 MPD.10: 5 residues within 4Å: Chain A: R.207, W.209 Chain C: F.260, Y.262, E.263 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.260, A:W.209 Hydrogen bonds: C:F.260 MPD.19: 6 residues within 4Å: Chain B: E.75, V.76, Q.77, D.101, F.102, Q.104 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Q.77 MPD.21: 5 residues within 4Å: Chain A: F.260, Y.262, E.263 Chain B: R.207, W.209 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:W.209, A:F.260 Hydrogen bonds: A:F.260 MPD.30: 6 residues within 4Å: Chain C: E.75, V.76, Q.77, D.101, F.102, Q.104 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Q.77 MPD.32: 5 residues within 4Å: Chain B: F.260, Y.262, E.263 Chain C: R.207, W.209 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:W.209, B:F.260 Hydrogen bonds: B:F.260 MPD.41: 6 residues within 4Å: Chain D: E.75, V.76, Q.77, D.101, F.102, Q.104 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:Q.77 MPD.43: 5 residues within 4Å: Chain D: R.207, W.209 Chain F: F.260, Y.262, E.263 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: F:F.260, D:W.209 Hydrogen bonds: F:F.260 MPD.52: 6 residues within 4Å: Chain E: E.75, V.76, Q.77, D.101, F.102, Q.104 1 PLIP interactions: 1 interactions with chain E Hydrophobic interactions: E:Q.77 MPD.54: 5 residues within 4Å: Chain D: F.260, Y.262, E.263 Chain E: R.207, W.209 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:F.260, E:W.209 Hydrogen bonds: D:F.260 MPD.63: 6 residues within 4Å: Chain F: E.75, V.76, Q.77, D.101, F.102, Q.104 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:Q.77 MPD.65: 5 residues within 4Å: Chain E: F.260, Y.262, E.263 Chain F: R.207, W.209 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:F.260, F:W.209 Hydrogen bonds: E:F.260

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

MRD.9: 5 residues within 4Å: Chain A: L.108, V.142, Q.180, N.202, L.241 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.108, A:V.142, A:L.241 Hydrogen bonds: A:Q.180 Water bridges: A:N.202 MRD.11: 8 residues within 4Å: Chain A: Y.215, L.216, P.217, R.257, F.260 Chain B: Y.288, E.289, L.290 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.288, B:E.289, B:L.290, A:L.216, A:L.216, A:F.260 Hydrogen bonds: B:L.290, B:L.290, A:Y.215 MRD.20: 5 residues within 4Å: Chain B: L.108, V.142, Q.180, N.202, L.241 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.108, B:V.142, B:L.241 Hydrogen bonds: B:Q.180 Water bridges: B:N.202 MRD.22: 8 residues within 4Å: Chain B: Y.215, L.216, P.217, R.257, F.260 Chain C: Y.288, E.289, L.290 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:L.216, B:L.216, B:F.260, C:Y.288, C:E.289, C:L.290 Hydrogen bonds: B:Y.215, C:L.290, C:L.290 MRD.31: 5 residues within 4Å: Chain C: L.108, V.142, Q.180, N.202, L.241 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:L.108, C:V.142, C:L.241 Hydrogen bonds: C:Q.180 Water bridges: C:N.202 MRD.33: 8 residues within 4Å: Chain A: Y.288, E.289, L.290 Chain C: Y.215, L.216, P.217, R.257, F.260 9 PLIP interactions: 4 interactions with chain C, 5 interactions with chain A Hydrophobic interactions: C:L.216, C:L.216, C:F.260, A:Y.288, A:E.289, A:L.290 Hydrogen bonds: C:Y.215, A:L.290, A:L.290 MRD.42: 5 residues within 4Å: Chain D: L.108, V.142, Q.180, N.202, L.241 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.108, D:V.142, D:L.241 Hydrogen bonds: D:Q.180 Water bridges: D:N.202 MRD.44: 8 residues within 4Å: Chain D: Y.215, L.216, P.217, R.257, F.260 Chain E: Y.288, E.289, L.290 10 PLIP interactions: 6 interactions with chain E, 4 interactions with chain D Hydrophobic interactions: E:Y.288, E:E.289, E:L.290, D:L.216, D:L.216, D:F.260 Hydrogen bonds: E:L.290, E:L.290, D:Y.215 Water bridges: E:E.289 MRD.53: 5 residues within 4Å: Chain E: L.108, V.142, Q.180, N.202, L.241 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:L.108, E:V.142, E:L.241 Hydrogen bonds: E:Q.180 Water bridges: E:N.202 MRD.55: 8 residues within 4Å: Chain E: Y.215, L.216, P.217, R.257, F.260 Chain F: Y.288, E.289, L.290 10 PLIP interactions: 4 interactions with chain E, 6 interactions with chain F Hydrophobic interactions: E:L.216, E:L.216, E:F.260, F:Y.288, F:E.289, F:L.290 Hydrogen bonds: E:Y.215, F:L.290, F:L.290 Water bridges: F:E.289 MRD.64: 5 residues within 4Å: Chain F: L.108, V.142, Q.180, N.202, L.241 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:L.108, F:V.142, F:L.241 Hydrogen bonds: F:Q.180 Water bridges: F:N.202 MRD.66: 8 residues within 4Å: Chain D: Y.288, E.289, L.290 Chain F: Y.215, L.216, P.217, R.257, F.260 10 PLIP interactions: 6 interactions with chain D, 4 interactions with chain F Hydrophobic interactions: D:Y.288, D:E.289, D:L.290, F:L.216, F:L.216, F:F.260 Hydrogen bonds: D:L.290, D:L.290, F:Y.215 Water bridges: D:E.289

Links

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Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of a putative phosphomethylpyrimidine kinase (BT_4458) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.10 A resolution (rhombohedral form). To be Published

Release Date

2010-05-12

Peptides

Putative phosphomethylpyrimidine kinase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Putative phosphomethylpyrimidine kinase

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