SMTL ID : 5fsd.1

1.75 A resolution 2,5-dihydroxybenzensulfonate inhibited Sporosarcina pasteurii urease

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

hetero-3-3-3-mer

Ligands

48 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.2: 7 residues within 4Å: Chain A: Y.32, M.76, I.77, D.78, D.79 Chain C: K.441 Chain D: M.1 Ligand excluded by PLIP EDO.3: 6 residues within 4Å: Chain A: K.24, G.27, L.28, K.29, D.67, D.68 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain B: D.101 Chain I: P.229, D.233, A.265 Ligand excluded by PLIP EDO.6: 2 residues within 4Å: Chain B: M.83, E.84 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain C: V.16, D.34, T.36, Y.38 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain C: Y.60, E.64, N.65, I.114 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain C: H.422, E.423, G.430 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain C: Y.93, E.423, R.513, I.514 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain C: P.143, G.189, P.191, R.478 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain C: F.570 Chain D: A.6, E.7, K.10, A.84, T.85, T.90 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain C: L.253, H.323, L.325, F.335 Chain E: Q.41 Chain F: G.46 Ligand excluded by PLIP EDO.18: 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 EDO.19: 7 residues within 4Å: Chain C: L.259, D.286, A.289, I.537, D.538, I.539 Chain E: R.38 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain C: Y.35, Y.83, I.97, E.429 Ligands: EDO.21 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain C: K.33, Y.35 Ligands: EDO.20 Ligand excluded by PLIP EDO.28: 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.29: 7 residues within 4Å: Chain D: Y.32, M.76, I.77, D.78, D.79 Chain F: K.441 Chain G: M.1 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain D: K.24, G.27, L.28, K.29, D.67, D.68 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain C: P.229, D.233, A.265 Chain E: D.101 Ligand excluded by PLIP EDO.33: 2 residues within 4Å: Chain E: M.83, E.84 Ligand excluded by PLIP EDO.38: 4 residues within 4Å: Chain F: V.16, D.34, T.36, Y.38 Ligand excluded by PLIP EDO.39: 4 residues within 4Å: Chain F: Y.60, E.64, N.65, I.114 Ligand excluded by PLIP EDO.40: 3 residues within 4Å: Chain F: H.422, E.423, G.430 Ligand excluded by PLIP EDO.41: 4 residues within 4Å: Chain F: Y.93, E.423, R.513, I.514 Ligand excluded by PLIP EDO.42: 4 residues within 4Å: Chain F: P.143, G.189, P.191, R.478 Ligand excluded by PLIP EDO.43: 7 residues within 4Å: Chain F: F.570 Chain G: A.6, E.7, K.10, A.84, T.85, T.90 Ligand excluded by PLIP EDO.44: 6 residues within 4Å: Chain F: L.253, H.323, L.325, F.335 Chain H: Q.41 Chain I: G.46 Ligand excluded by PLIP EDO.45: 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 EDO.46: 7 residues within 4Å: Chain F: L.259, D.286, A.289, I.537, D.538, I.539 Chain H: R.38 Ligand excluded by PLIP EDO.47: 5 residues within 4Å: Chain F: Y.35, Y.83, I.97, E.429 Ligands: EDO.48 Ligand excluded by PLIP EDO.48: 3 residues within 4Å: Chain F: K.33, Y.35 Ligands: EDO.47 Ligand excluded by PLIP EDO.55: 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.56: 7 residues within 4Å: Chain A: M.1 Chain G: Y.32, M.76, I.77, D.78, D.79 Chain I: K.441 Ligand excluded by PLIP EDO.57: 6 residues within 4Å: Chain G: K.24, G.27, L.28, K.29, D.67, D.68 Ligand excluded by PLIP EDO.59: 4 residues within 4Å: Chain F: P.229, D.233, A.265 Chain H: D.101 Ligand excluded by PLIP EDO.60: 2 residues within 4Å: Chain H: M.83, E.84 Ligand excluded by PLIP EDO.65: 4 residues within 4Å: Chain I: V.16, D.34, T.36, Y.38 Ligand excluded by PLIP EDO.66: 4 residues within 4Å: Chain I: Y.60, E.64, N.65, I.114 Ligand excluded by PLIP EDO.67: 3 residues within 4Å: Chain I: H.422, E.423, G.430 Ligand excluded by PLIP EDO.68: 4 residues within 4Å: Chain I: Y.93, E.423, R.513, I.514 Ligand excluded by PLIP EDO.69: 4 residues within 4Å: Chain I: P.143, G.189, P.191, R.478 Ligand excluded by PLIP EDO.70: 7 residues within 4Å: Chain A: A.6, E.7, K.10, A.84, T.85, T.90 Chain I: F.570 Ligand excluded by PLIP EDO.71: 6 residues within 4Å: Chain B: Q.41 Chain C: G.46 Chain I: L.253, H.323, L.325, F.335 Ligand excluded by PLIP EDO.72: 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 EDO.73: 7 residues within 4Å: Chain B: R.38 Chain I: L.259, D.286, A.289, I.537, D.538, I.539 Ligand excluded by PLIP EDO.74: 5 residues within 4Å: Chain I: Y.35, Y.83, I.97, E.429 Ligands: EDO.75 Ligand excluded by PLIP EDO.75: 3 residues within 4Å: Chain I: K.33, Y.35 Ligands: EDO.74 Ligand excluded by PLIP

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

SO4.4: 3 residues within 4Å: Chain A: M.70, E.71 Chain C: R.566 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain B: L.112, R.116 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain B: T.29, I.30, R.31 Ligand excluded by PLIP SO4.22: 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 SO4.24: 2 residues within 4Å: Chain C: S.204, I.205 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain C: V.558, K.559, E.560 Ligand excluded by PLIP SO4.31: 3 residues within 4Å: Chain D: M.70, E.71 Chain F: R.566 Ligand excluded by PLIP SO4.34: 2 residues within 4Å: Chain E: L.112, R.116 Ligand excluded by PLIP SO4.35: 3 residues within 4Å: Chain E: T.29, I.30, R.31 Ligand excluded by PLIP SO4.49: 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 SO4.51: 2 residues within 4Å: Chain F: S.204, I.205 Ligand excluded by PLIP SO4.52: 3 residues within 4Å: Chain F: V.558, K.559, E.560 Ligand excluded by PLIP SO4.58: 3 residues within 4Å: Chain G: M.70, E.71 Chain I: R.566 Ligand excluded by PLIP SO4.61: 2 residues within 4Å: Chain H: L.112, R.116 Ligand excluded by PLIP SO4.62: 3 residues within 4Å: Chain H: T.29, I.30, R.31 Ligand excluded by PLIP SO4.76: 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 SO4.78: 2 residues within 4Å: Chain I: S.204, I.205 Ligand excluded by PLIP SO4.79: 3 residues within 4Å: Chain I: V.558, K.559, E.560 Ligand excluded by PLIP

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

NI.9: 8 residues within 4Å: Chain C: H.137, K.220, H.222, H.249, H.275, G.280 Ligands: NI.10, OH.23 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.15, OH.23 NI.10: 6 residues within 4Å: Chain C: H.137, H.139, K.220, D.363 Ligands: NI.9, OH.23 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.15, OH.23 NI.36: 8 residues within 4Å: Chain F: H.137, K.220, H.222, H.249, H.275, G.280 Ligands: NI.37, OH.50 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.40, OH.50 NI.37: 6 residues within 4Å: Chain F: H.137, H.139, K.220, D.363 Ligands: NI.36, OH.50 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.39, OH.50 NI.63: 8 residues within 4Å: Chain I: H.137, K.220, H.222, H.249, H.275, G.280 Ligands: NI.64, OH.77 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.65, OH.77 NI.64: 6 residues within 4Å: Chain I: H.137, H.139, K.220, D.363 Ligands: NI.63, OH.77 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.64, OH.77

3 x OH: HYDROXIDE ION(Non-covalent)

OH.23: 8 residues within 4Å: Chain C: H.137, K.220, H.249, H.275, G.280, D.363 Ligands: NI.9, NI.10 No protein-ligand interaction detected (PLIP) OH.50: 8 residues within 4Å: Chain F: H.137, K.220, H.249, H.275, G.280, D.363 Ligands: NI.36, NI.37 No protein-ligand interaction detected (PLIP) OH.77: 8 residues within 4Å: Chain I: H.137, K.220, H.249, H.275, G.280, D.363 Ligands: NI.63, NI.64 No protein-ligand interaction detected (PLIP)

6 x DBX: 2,5-dihydroxybenzenesulfonic acid(Covalent)

DBX.26: 7 residues within 4Å: Chain C: K.169, V.321, C.322 Chain D: Q.81 Chain F: I.468, P.469, T.470 9 PLIP interactions: 4 interactions with chain C, 4 interactions with chain F, 1 interactions with chain D Water bridges: C:E.166, C:K.169, C:K.169 Salt bridges: C:K.169 Hydrophobic interactions: F:I.468, F:I.468, F:T.470 Hydrogen bonds: F:T.470, D:Q.81 DBX.27: 6 residues within 4Å: Chain C: I.350, Q.387, R.388, T.554, C.555, E.556 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:I.350 Hydrogen bonds: C:E.556 Water bridges: C:Q.387 DBX.53: 7 residues within 4Å: Chain F: K.169, V.321, C.322 Chain G: Q.81 Chain I: I.468, P.469, T.470 9 PLIP interactions: 4 interactions with chain F, 4 interactions with chain I, 1 interactions with chain G Water bridges: F:E.166, F:K.169, F:K.169 Salt bridges: F:K.169 Hydrophobic interactions: I:I.468, I:I.468, I:T.470 Hydrogen bonds: I:T.470, G:Q.81 DBX.54: 6 residues within 4Å: Chain F: I.350, Q.387, R.388, T.554, C.555, E.556 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:I.350 Hydrogen bonds: F:E.556 Water bridges: F:Q.387 DBX.80: 7 residues within 4Å: Chain A: Q.81 Chain C: I.468, P.469, T.470 Chain I: K.169, V.321, C.322 9 PLIP interactions: 4 interactions with chain I, 1 interactions with chain A, 4 interactions with chain C Water bridges: I:E.166, I:K.169, I:K.169 Salt bridges: I:K.169 Hydrogen bonds: A:Q.81, C:T.470 Hydrophobic interactions: C:I.468, C:I.468, C:T.470 DBX.81: 6 residues within 4Å: Chain I: I.350, Q.387, R.388, T.554, C.555, E.556 3 PLIP interactions: 3 interactions with chain I Hydrophobic interactions: I:I.350 Hydrogen bonds: I:E.556 Water bridges: I:Q.387

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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