SMTL ID : 5fse.1

2.07 A resolution 1,4-Benzoquinone inhibited Sporosarcina pasteurii urease

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

hetero-3-3-3-mer

Ligands

30 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.1: 9 residues within 4Å: Chain A: G.50, K.51, T.52, F.86, P.87, D.88 Chain I: V.309, N.310, K.559 Ligand excluded by PLIP EDO.3: 3 residues within 4Å: Chain B: I.69, V.85, E.86 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain C: D.286, A.289, I.537, D.538, I.539 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain C: T.36, T.37, Y.38 Ligands: EDO.11 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain C: Y.60, N.65, I.114 Ligands: SO4.18 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain C: P.143, G.189, L.190, R.478 Chain F: V.483 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain C: D.34, T.36, Y.38 Ligands: EDO.8 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain C: R.513, I.514 Ligands: EDO.14 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain C: K.33, D.34, Y.35 Ligands: SO4.17 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain C: Y.93, E.423, R.513, I.514 Ligands: EDO.12 Ligand excluded by PLIP EDO.25: 9 residues within 4Å: Chain C: V.309, N.310, K.559 Chain D: G.50, K.51, T.52, F.86, P.87, D.88 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain E: I.69, V.85, E.86 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain F: D.286, A.289, I.537, D.538, I.539 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain F: T.36, T.37, Y.38 Ligands: EDO.35 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain F: Y.60, N.65, I.114 Ligands: SO4.42 Ligand excluded by PLIP EDO.34: 5 residues within 4Å: Chain F: P.143, G.189, L.190, R.478 Chain I: V.483 Ligand excluded by PLIP EDO.35: 4 residues within 4Å: Chain F: D.34, T.36, Y.38 Ligands: EDO.32 Ligand excluded by PLIP EDO.36: 3 residues within 4Å: Chain F: R.513, I.514 Ligands: EDO.38 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain F: K.33, D.34, Y.35 Ligands: SO4.41 Ligand excluded by PLIP EDO.38: 5 residues within 4Å: Chain F: Y.93, E.423, R.513, I.514 Ligands: EDO.36 Ligand excluded by PLIP EDO.49: 9 residues within 4Å: Chain F: V.309, N.310, K.559 Chain G: G.50, K.51, T.52, F.86, P.87, D.88 Ligand excluded by PLIP EDO.51: 3 residues within 4Å: Chain H: I.69, V.85, E.86 Ligand excluded by PLIP EDO.55: 5 residues within 4Å: Chain I: D.286, A.289, I.537, D.538, I.539 Ligand excluded by PLIP EDO.56: 4 residues within 4Å: Chain I: T.36, T.37, Y.38 Ligands: EDO.59 Ligand excluded by PLIP EDO.57: 4 residues within 4Å: Chain I: Y.60, N.65, I.114 Ligands: SO4.66 Ligand excluded by PLIP EDO.58: 5 residues within 4Å: Chain C: V.483 Chain I: P.143, G.189, L.190, R.478 Ligand excluded by PLIP EDO.59: 4 residues within 4Å: Chain I: D.34, T.36, Y.38 Ligands: EDO.56 Ligand excluded by PLIP EDO.60: 3 residues within 4Å: Chain I: R.513, I.514 Ligands: EDO.62 Ligand excluded by PLIP EDO.61: 4 residues within 4Å: Chain I: K.33, D.34, Y.35 Ligands: SO4.65 Ligand excluded by PLIP EDO.62: 5 residues within 4Å: Chain I: Y.93, E.423, R.513, I.514 Ligands: EDO.60 Ligand excluded by PLIP

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

SO4.2: 3 residues within 4Å: Chain A: M.70, E.71 Chain C: R.566 Ligand excluded by PLIP SO4.4: 2 residues within 4Å: Chain B: L.112, R.116 Ligand excluded by PLIP SO4.15: 8 residues within 4Å: Chain C: A.170, H.222, E.223, D.224, H.249, G.280, H.323, R.339 Ligand excluded by PLIP SO4.17: 3 residues within 4Å: Chain C: K.33, Y.35 Ligands: EDO.13 Ligand excluded by PLIP SO4.18: 1 residues within 4Å: Ligands: EDO.9 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain C: V.558, K.559, E.560 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain C: M.106, D.107, G.108, V.109 Ligand excluded by PLIP SO4.23: 7 residues within 4Å: Chain B: S.71, G.72, T.73 Chain C: S.11, Y.12, N.43, K.48 Ligand excluded by PLIP SO4.24: 2 residues within 4Å: Chain C: R.388 Ligands: HQE.19 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain D: M.70, E.71 Chain F: R.566 Ligand excluded by PLIP SO4.28: 2 residues within 4Å: Chain E: L.112, R.116 Ligand excluded by PLIP SO4.39: 8 residues within 4Å: Chain F: A.170, H.222, E.223, D.224, H.249, G.280, H.323, R.339 Ligand excluded by PLIP SO4.41: 3 residues within 4Å: Chain F: K.33, Y.35 Ligands: EDO.37 Ligand excluded by PLIP SO4.42: 1 residues within 4Å: Ligands: EDO.33 Ligand excluded by PLIP SO4.45: 3 residues within 4Å: Chain F: V.558, K.559, E.560 Ligand excluded by PLIP SO4.46: 4 residues within 4Å: Chain F: M.106, D.107, G.108, V.109 Ligand excluded by PLIP SO4.47: 7 residues within 4Å: Chain E: S.71, G.72, T.73 Chain F: S.11, Y.12, N.43, K.48 Ligand excluded by PLIP SO4.48: 2 residues within 4Å: Chain F: R.388 Ligands: HQE.43 Ligand excluded by PLIP SO4.50: 3 residues within 4Å: Chain G: M.70, E.71 Chain I: R.566 Ligand excluded by PLIP SO4.52: 2 residues within 4Å: Chain H: L.112, R.116 Ligand excluded by PLIP SO4.63: 8 residues within 4Å: Chain I: A.170, H.222, E.223, D.224, H.249, G.280, H.323, R.339 Ligand excluded by PLIP SO4.65: 3 residues within 4Å: Chain I: K.33, Y.35 Ligands: EDO.61 Ligand excluded by PLIP SO4.66: 1 residues within 4Å: Ligands: EDO.57 Ligand excluded by PLIP SO4.69: 3 residues within 4Å: Chain I: V.558, K.559, E.560 Ligand excluded by PLIP SO4.70: 4 residues within 4Å: Chain I: M.106, D.107, G.108, V.109 Ligand excluded by PLIP SO4.71: 7 residues within 4Å: Chain H: S.71, G.72, T.73 Chain I: S.11, Y.12, N.43, K.48 Ligand excluded by PLIP SO4.72: 2 residues within 4Å: Chain I: R.388 Ligands: HQE.67 Ligand excluded by PLIP

6 x NI: NICKEL (II) ION(Non-covalent)

NI.5: 8 residues within 4Å: Chain C: H.137, K.220, H.222, H.249, H.275, G.280 Ligands: NI.6, OH.16 4 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: C:H.249, C:H.275, H2O.11, OH.16 NI.6: 6 residues within 4Å: Chain C: H.137, H.139, K.220, D.363 Ligands: NI.5, OH.16 5 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: C:H.137, C:H.139, C:D.363, H2O.10, OH.16 NI.29: 8 residues within 4Å: Chain F: H.137, K.220, H.222, H.249, H.275, G.280 Ligands: NI.30, OH.40 4 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: F:H.249, F:H.275, H2O.29, OH.40 NI.30: 6 residues within 4Å: Chain F: H.137, H.139, K.220, D.363 Ligands: NI.29, OH.40 5 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: F:H.137, F:H.139, F:D.363, H2O.28, OH.40 NI.53: 8 residues within 4Å: Chain I: H.137, K.220, H.222, H.249, H.275, G.280 Ligands: NI.54, OH.64 4 PLIP interactions: 2 interactions with chain I, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: I:H.249, I:H.275, H2O.47, OH.64 NI.54: 6 residues within 4Å: Chain I: H.137, H.139, K.220, D.363 Ligands: NI.53, OH.64 5 PLIP interactions: 3 interactions with chain I, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: I:H.137, I:H.139, I:D.363, H2O.46, OH.64

3 x OH: HYDROXIDE ION(Non-covalent)

OH.16: 8 residues within 4Å: Chain C: H.137, K.220, H.249, H.275, G.280, D.363 Ligands: NI.5, NI.6 No protein-ligand interaction detected (PLIP) OH.40: 8 residues within 4Å: Chain F: H.137, K.220, H.249, H.275, G.280, D.363 Ligands: NI.29, NI.30 No protein-ligand interaction detected (PLIP) OH.64: 8 residues within 4Å: Chain I: H.137, K.220, H.249, H.275, G.280, D.363 Ligands: NI.53, NI.54 No protein-ligand interaction detected (PLIP)

6 x HQE: benzene-1,4-diol(Covalent)

HQE.19: 7 residues within 4Å: Chain C: I.350, Q.387, R.388, T.554, C.555, E.556 Ligands: SO4.24 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:I.350, C:Q.387 Hydrogen bonds: C:R.388, C:E.556, C:E.556 HQE.20: 6 residues within 4Å: Chain C: V.321, C.322 Chain D: Q.81 Chain F: I.468, P.469, T.470 6 PLIP interactions: 2 interactions with chain C, 4 interactions with chain F Hydrogen bonds: C:V.321, F:T.470 Water bridges: C:K.169 Hydrophobic interactions: F:I.468, F:I.468, F:T.470 HQE.43: 7 residues within 4Å: Chain F: I.350, Q.387, R.388, T.554, C.555, E.556 Ligands: SO4.48 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:I.350, F:Q.387 Hydrogen bonds: F:R.388, F:E.556, F:E.556 HQE.44: 6 residues within 4Å: Chain F: V.321, C.322 Chain G: Q.81 Chain I: I.468, P.469, T.470 6 PLIP interactions: 2 interactions with chain F, 4 interactions with chain I Hydrogen bonds: F:V.321, I:T.470 Water bridges: F:K.169 Hydrophobic interactions: I:I.468, I:I.468, I:T.470 HQE.67: 7 residues within 4Å: Chain I: I.350, Q.387, R.388, T.554, C.555, E.556 Ligands: SO4.72 5 PLIP interactions: 5 interactions with chain I Hydrophobic interactions: I:I.350, I:Q.387 Hydrogen bonds: I:R.388, I:E.556, I:E.556 HQE.68: 6 residues within 4Å: Chain A: Q.81 Chain C: I.468, P.469, T.470 Chain I: V.321, C.322 6 PLIP interactions: 4 interactions with chain C, 2 interactions with chain I Hydrophobic interactions: C:I.468, C:I.468, C:T.470 Hydrogen bonds: C:T.470, I:V.321 Water bridges: I:K.169

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mazzei, L. et al., Inactivation of Urease by 1,4-Benzoquinone: Chemistry at the Protein Surface. Dalton Trans (2016)

Release Date

2016-03-23

Peptides

UREASE SUBUNIT GAMMA: ADG
UREASE SUBUNIT BETA: BEH
UREASE SUBUNIT ALPHA: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

G
A

B
B

E
B

H
B

C
C

F
C

I
C

UREASE SUBUNIT GAMMA

UREASE SUBUNIT BETA

UREASE SUBUNIT ALPHA

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