SMTL ID : 2i1o.1

Crystal Structure of a Nicotinate Phosphoribosyltransferase from Thermoplasma acidophilum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-hexamer

Ligands

36 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 5 residues within 4Å: Chain A: M.186, T.203 Chain F: R.30, T.31, A.34 Ligand excluded by PLIP PO4.2: 8 residues within 4Å: Chain A: M.186, P.187, H.188, L.216, R.241, D.243 Chain F: Y.27 Ligands: MPD.10 Ligand excluded by PLIP PO4.3: 5 residues within 4Å: Chain A: P.53, G.124, A.304, K.305, F.307 Ligand excluded by PLIP PO4.4: 4 residues within 4Å: Chain A: R.249, G.250, N.251, F.252 Ligand excluded by PLIP PO4.5: 2 residues within 4Å: Chain A: C.339, H.340 Ligand excluded by PLIP PO4.6: 5 residues within 4Å: Chain A: R.335, C.336, T.337, H.340, Y.393 Ligand excluded by PLIP PO4.14: 5 residues within 4Å: Chain B: M.186, T.203 Chain E: R.30, T.31, A.34 Ligand excluded by PLIP PO4.15: 8 residues within 4Å: Chain B: M.186, P.187, H.188, L.216, R.241, D.243 Chain E: Y.27 Ligands: MPD.23 Ligand excluded by PLIP PO4.16: 5 residues within 4Å: Chain B: P.53, G.124, A.304, K.305, F.307 Ligand excluded by PLIP PO4.17: 4 residues within 4Å: Chain B: R.249, G.250, N.251, F.252 Ligand excluded by PLIP PO4.18: 2 residues within 4Å: Chain B: C.339, H.340 Ligand excluded by PLIP PO4.19: 5 residues within 4Å: Chain B: R.335, C.336, T.337, H.340, Y.393 Ligand excluded by PLIP PO4.27: 5 residues within 4Å: Chain C: M.186, T.203 Chain D: R.30, T.31, A.34 Ligand excluded by PLIP PO4.28: 8 residues within 4Å: Chain C: M.186, P.187, H.188, L.216, R.241, D.243 Chain D: Y.27 Ligands: MPD.36 Ligand excluded by PLIP PO4.29: 5 residues within 4Å: Chain C: P.53, G.124, A.304, K.305, F.307 Ligand excluded by PLIP PO4.30: 4 residues within 4Å: Chain C: R.249, G.250, N.251, F.252 Ligand excluded by PLIP PO4.31: 2 residues within 4Å: Chain C: C.339, H.340 Ligand excluded by PLIP PO4.32: 5 residues within 4Å: Chain C: R.335, C.336, T.337, H.340, Y.393 Ligand excluded by PLIP PO4.40: 5 residues within 4Å: Chain C: R.30, T.31, A.34 Chain D: M.186, T.203 Ligand excluded by PLIP PO4.41: 8 residues within 4Å: Chain C: Y.27 Chain D: M.186, P.187, H.188, L.216, R.241, D.243 Ligands: MPD.49 Ligand excluded by PLIP PO4.42: 5 residues within 4Å: Chain D: P.53, G.124, A.304, K.305, F.307 Ligand excluded by PLIP PO4.43: 4 residues within 4Å: Chain D: R.249, G.250, N.251, F.252 Ligand excluded by PLIP PO4.44: 2 residues within 4Å: Chain D: C.339, H.340 Ligand excluded by PLIP PO4.45: 5 residues within 4Å: Chain D: R.335, C.336, T.337, H.340, Y.393 Ligand excluded by PLIP PO4.53: 5 residues within 4Å: Chain B: R.30, T.31, A.34 Chain E: M.186, T.203 Ligand excluded by PLIP PO4.54: 8 residues within 4Å: Chain B: Y.27 Chain E: M.186, P.187, H.188, L.216, R.241, D.243 Ligands: MPD.62 Ligand excluded by PLIP PO4.55: 5 residues within 4Å: Chain E: P.53, G.124, A.304, K.305, F.307 Ligand excluded by PLIP PO4.56: 4 residues within 4Å: Chain E: R.249, G.250, N.251, F.252 Ligand excluded by PLIP PO4.57: 2 residues within 4Å: Chain E: C.339, H.340 Ligand excluded by PLIP PO4.58: 5 residues within 4Å: Chain E: R.335, C.336, T.337, H.340, Y.393 Ligand excluded by PLIP PO4.66: 5 residues within 4Å: Chain A: R.30, T.31, A.34 Chain F: M.186, T.203 Ligand excluded by PLIP PO4.67: 8 residues within 4Å: Chain A: Y.27 Chain F: M.186, P.187, H.188, L.216, R.241, D.243 Ligands: MPD.75 Ligand excluded by PLIP PO4.68: 5 residues within 4Å: Chain F: P.53, G.124, A.304, K.305, F.307 Ligand excluded by PLIP PO4.69: 4 residues within 4Å: Chain F: R.249, G.250, N.251, F.252 Ligand excluded by PLIP PO4.70: 2 residues within 4Å: Chain F: C.339, H.340 Ligand excluded by PLIP PO4.71: 5 residues within 4Å: Chain F: R.335, C.336, T.337, H.340, Y.393 Ligand excluded by PLIP

12 x ZN: ZINC ION(Non-covalent)

ZN.7: 6 residues within 4Å: Chain A: C.336, S.338, C.339, C.356, G.357 Ligands: ZN.8 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.336, A:C.339, A:C.356 ZN.8: 7 residues within 4Å: Chain A: C.336, C.354, C.356, G.357, S.359, M.360 Ligands: ZN.7 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.336, A:C.354, A:C.356 ZN.20: 6 residues within 4Å: Chain B: C.336, S.338, C.339, C.356, G.357 Ligands: ZN.21 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.336, B:C.339, B:C.356 ZN.21: 7 residues within 4Å: Chain B: C.336, C.354, C.356, G.357, S.359, M.360 Ligands: ZN.20 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.336, B:C.354, B:C.356 ZN.33: 6 residues within 4Å: Chain C: C.336, S.338, C.339, C.356, G.357 Ligands: ZN.34 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.336, C:C.339, C:C.356 ZN.34: 7 residues within 4Å: Chain C: C.336, C.354, C.356, G.357, S.359, M.360 Ligands: ZN.33 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:C.336, C:C.354, C:C.356 ZN.46: 6 residues within 4Å: Chain D: C.336, S.338, C.339, C.356, G.357 Ligands: ZN.47 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.336, D:C.339, D:C.356 ZN.47: 7 residues within 4Å: Chain D: C.336, C.354, C.356, G.357, S.359, M.360 Ligands: ZN.46 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:C.336, D:C.354, D:C.356 ZN.59: 6 residues within 4Å: Chain E: C.336, S.338, C.339, C.356, G.357 Ligands: ZN.60 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.336, E:C.339, E:C.356 ZN.60: 7 residues within 4Å: Chain E: C.336, C.354, C.356, G.357, S.359, M.360 Ligands: ZN.59 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:C.336, E:C.354, E:C.356 ZN.72: 6 residues within 4Å: Chain F: C.336, S.338, C.339, C.356, G.357 Ligands: ZN.73 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.336, F:C.339, F:C.356 ZN.73: 7 residues within 4Å: Chain F: C.336, C.354, C.356, G.357, S.359, M.360 Ligands: ZN.72 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:C.336, F:C.354, F:C.356

6 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.9: 7 residues within 4Å: Chain A: R.148, G.277, G.278, L.279, G.296, G.298, T.299 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.148, A:G.277, A:G.278, A:L.279, A:G.296, A:G.298, A:T.299, A:T.299, A:T.299 Water bridges: A:S.300 TRS.22: 7 residues within 4Å: Chain B: R.148, G.277, G.278, L.279, G.296, G.298, T.299 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.148, B:G.277, B:G.278, B:L.279, B:G.296, B:G.298, B:T.299, B:T.299, B:T.299 Water bridges: B:S.300 TRS.35: 7 residues within 4Å: Chain C: R.148, G.277, G.278, L.279, G.296, G.298, T.299 10 PLIP interactions: 10 interactions with chain C Hydrogen bonds: C:R.148, C:G.277, C:G.278, C:L.279, C:G.296, C:G.298, C:T.299, C:T.299, C:T.299 Water bridges: C:S.300 TRS.48: 7 residues within 4Å: Chain D: R.148, G.277, G.278, L.279, G.296, G.298, T.299 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:R.148, D:G.277, D:G.278, D:L.279, D:G.296, D:G.298, D:T.299, D:T.299 Water bridges: D:S.300 TRS.61: 7 residues within 4Å: Chain E: R.148, G.277, G.278, L.279, G.296, G.298, T.299 9 PLIP interactions: 9 interactions with chain E Hydrogen bonds: E:R.148, E:G.277, E:G.278, E:L.279, E:G.296, E:G.298, E:T.299, E:T.299 Water bridges: E:S.300 TRS.74: 7 residues within 4Å: Chain F: R.148, G.277, G.278, L.279, G.296, G.298, T.299 9 PLIP interactions: 9 interactions with chain F Hydrogen bonds: F:R.148, F:G.277, F:G.278, F:L.279, F:G.296, F:G.298, F:T.299, F:T.299 Water bridges: F:S.300

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

MPD.10: 8 residues within 4Å: Chain A: F.144, R.147, S.170, T.185, R.241 Chain F: D.25, Y.27 Ligands: PO4.2 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain F Hydrophobic interactions: A:F.144, F:Y.27 Hydrogen bonds: A:R.147, A:R.241, A:R.241 MPD.11: 6 residues within 4Å: Chain A: F.142, V.183, K.212, V.214, Y.239, M.274 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.142, A:K.212, A:V.214, A:Y.239 Water bridges: A:G.184, A:G.184 MPD.23: 8 residues within 4Å: Chain B: F.144, R.147, S.170, T.185, R.241 Chain E: D.25, Y.27 Ligands: PO4.15 5 PLIP interactions: 1 interactions with chain E, 4 interactions with chain B Hydrophobic interactions: E:Y.27, B:F.144 Hydrogen bonds: B:R.147, B:R.241, B:R.241 MPD.24: 6 residues within 4Å: Chain B: F.142, V.183, K.212, V.214, Y.239, M.274 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.142, B:K.212, B:V.214, B:Y.239 Water bridges: B:G.184, B:G.184 MPD.36: 8 residues within 4Å: Chain C: F.144, R.147, S.170, T.185, R.241 Chain D: D.25, Y.27 Ligands: PO4.28 5 PLIP interactions: 1 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:Y.27, C:F.144 Hydrogen bonds: C:R.147, C:R.241, C:R.241 MPD.37: 6 residues within 4Å: Chain C: F.142, V.183, K.212, V.214, Y.239, M.274 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.142, C:K.212, C:V.214, C:Y.239 Water bridges: C:G.184, C:G.184 MPD.49: 8 residues within 4Å: Chain C: D.25, Y.27 Chain D: F.144, R.147, S.170, T.185, R.241 Ligands: PO4.41 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.144, C:Y.27 Hydrogen bonds: D:R.147, D:R.241, D:R.241 MPD.50: 6 residues within 4Å: Chain D: F.142, V.183, K.212, V.214, Y.239, M.274 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.142, D:K.212, D:V.214, D:Y.239 Water bridges: D:G.184, D:G.184 MPD.62: 8 residues within 4Å: Chain B: D.25, Y.27 Chain E: F.144, R.147, S.170, T.185, R.241 Ligands: PO4.54 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain B Hydrophobic interactions: E:F.144, B:Y.27 Hydrogen bonds: E:R.147, E:R.241, E:R.241 MPD.63: 6 residues within 4Å: Chain E: F.142, V.183, K.212, V.214, Y.239, M.274 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:F.142, E:K.212, E:V.214, E:Y.239 Water bridges: E:G.184, E:G.184 MPD.75: 8 residues within 4Å: Chain A: D.25, Y.27 Chain F: F.144, R.147, S.170, T.185, R.241 Ligands: PO4.67 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain A Hydrophobic interactions: F:F.144, A:Y.27 Hydrogen bonds: F:R.147, F:R.241, F:R.241 MPD.76: 6 residues within 4Å: Chain F: F.142, V.183, K.212, V.214, Y.239, M.274 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:F.142, F:K.212, F:V.214, F:Y.239 Water bridges: F:G.184, F:G.184

12 x ACY: ACETIC ACID(Non-functional Binders)

ACY.12: 2 residues within 4Å: Chain A: G.278, D.280 No protein-ligand interaction detected (PLIP) ACY.13: 4 residues within 4Å: Chain A: R.43, D.74, D.76, H.370 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.370 ACY.25: 2 residues within 4Å: Chain B: G.278, D.280 No protein-ligand interaction detected (PLIP) ACY.26: 4 residues within 4Å: Chain B: R.43, D.74, D.76, H.370 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.370 ACY.38: 2 residues within 4Å: Chain C: G.278, D.280 No protein-ligand interaction detected (PLIP) ACY.39: 4 residues within 4Å: Chain C: R.43, D.74, D.76, H.370 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:H.370 ACY.51: 2 residues within 4Å: Chain D: G.278, D.280 No protein-ligand interaction detected (PLIP) ACY.52: 4 residues within 4Å: Chain D: R.43, D.74, D.76, H.370 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:H.370 ACY.64: 2 residues within 4Å: Chain E: G.278, D.280 No protein-ligand interaction detected (PLIP) ACY.65: 4 residues within 4Å: Chain E: R.43, D.74, D.76, H.370 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:H.370 ACY.77: 2 residues within 4Å: Chain F: G.278, D.280 No protein-ligand interaction detected (PLIP) ACY.78: 4 residues within 4Å: Chain F: R.43, D.74, D.76, H.370 1 PLIP interactions: 1 interactions with chain F Salt bridges: F:H.370

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shin, D.H. et al., Crystal Structure of a zinc ion bound Nicotinate Phosphoribosyltransferase from Thermoplasma acidophilum. To be Published

Release Date

2006-08-29

Peptides

Nicotinate Phosphoribosyltransferase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Nicotinate Phosphoribosyltransferase

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