SMTL ID : 6i9y.1

The 2.14 A X-ray crystal structure of Sporosarcina pasteurii urease in complex with Au(I) ions

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

hetero-3-3-3-mer

Ligands

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

EDO.1: 8 residues within 4Å: Chain A: G.50, K.51, T.52, F.86, P.87 Chain F: V.309, N.310, K.559 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain B: S.96, D.97 Chain F: P.229, D.233 Ligands: EDO.48 Ligand excluded by PLIP EDO.5: 2 residues within 4Å: Chain B: M.79, E.80 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain C: S.204, I.205, A.206 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain C: D.286, A.289, I.537, D.538, I.539 Chain H: R.34 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain C: H.293, P.294, N.295 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain C: F.307, P.342, E.343, A.346, C.555 Ligand excluded by PLIP EDO.15: 7 residues within 4Å: Chain B: S.67, G.68, T.69 Chain C: S.11, Y.12, N.43, K.48 Ligand excluded by PLIP EDO.16: 3 residues within 4Å: Chain C: D.34, T.36, Y.38 Ligand excluded by PLIP EDO.23: 6 residues within 4Å: Chain C: D.224, H.323 Chain I: G.45, G.46, K.48 Ligands: SO4.22 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain C: D.233, R.264, A.265, N.267, R.269 Ligands: EDO.52 Ligand excluded by PLIP EDO.25: 8 residues within 4Å: Chain D: G.50, K.51, T.52, F.86, P.87 Chain I: V.309, N.310, K.559 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain E: S.96, D.97 Chain I: P.229, D.233 Ligands: EDO.72 Ligand excluded by PLIP EDO.29: 2 residues within 4Å: Chain E: M.79, E.80 Ligand excluded by PLIP EDO.35: 3 residues within 4Å: Chain F: S.204, I.205, A.206 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain B: R.34 Chain F: D.286, A.289, I.537, D.538, I.539 Ligand excluded by PLIP EDO.37: 3 residues within 4Å: Chain F: H.293, P.294, N.295 Ligand excluded by PLIP EDO.38: 5 residues within 4Å: Chain F: F.307, P.342, E.343, A.346, C.555 Ligand excluded by PLIP EDO.39: 7 residues within 4Å: Chain E: S.67, G.68, T.69 Chain F: S.11, Y.12, N.43, K.48 Ligand excluded by PLIP EDO.40: 3 residues within 4Å: Chain F: D.34, T.36, Y.38 Ligand excluded by PLIP EDO.47: 6 residues within 4Å: Chain C: G.45, G.46, K.48 Chain F: D.224, H.323 Ligands: SO4.46 Ligand excluded by PLIP EDO.48: 6 residues within 4Å: Chain F: D.233, R.264, A.265, N.267, R.269 Ligands: EDO.4 Ligand excluded by PLIP EDO.49: 8 residues within 4Å: Chain C: V.309, N.310, K.559 Chain G: G.50, K.51, T.52, F.86, P.87 Ligand excluded by PLIP EDO.52: 5 residues within 4Å: Chain C: P.229, D.233 Chain H: S.96, D.97 Ligands: EDO.24 Ligand excluded by PLIP EDO.53: 2 residues within 4Å: Chain H: M.79, E.80 Ligand excluded by PLIP EDO.59: 3 residues within 4Å: Chain I: S.204, I.205, A.206 Ligand excluded by PLIP EDO.60: 6 residues within 4Å: Chain E: R.34 Chain I: D.286, A.289, I.537, D.538, I.539 Ligand excluded by PLIP EDO.61: 3 residues within 4Å: Chain I: H.293, P.294, N.295 Ligand excluded by PLIP EDO.62: 5 residues within 4Å: Chain I: F.307, P.342, E.343, A.346, C.555 Ligand excluded by PLIP EDO.63: 7 residues within 4Å: Chain H: S.67, G.68, T.69 Chain I: S.11, Y.12, N.43, K.48 Ligand excluded by PLIP EDO.64: 3 residues within 4Å: Chain I: D.34, T.36, Y.38 Ligand excluded by PLIP EDO.71: 6 residues within 4Å: Chain F: G.45, G.46, K.48 Chain I: D.224, H.323 Ligands: SO4.70 Ligand excluded by PLIP EDO.72: 6 residues within 4Å: Chain I: D.233, R.264, A.265, N.267, R.269 Ligands: EDO.28 Ligand excluded by PLIP

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

SO4.2: 3 residues within 4Å: Chain A: A.54, M.57, E.58 Ligand excluded by PLIP SO4.3: 8 residues within 4Å: Chain A: A.6, E.7, K.10, T.85, T.90 Chain C: S.465 Chain F: F.568, F.570 Ligand excluded by PLIP SO4.6: 2 residues within 4Å: Chain B: I.26, R.27 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain B: L.108, R.112 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain C: Y.35, Y.83, I.97, E.429 Ligand excluded by PLIP SO4.18: 2 residues within 4Å: Chain C: I.500, Q.501 Ligand excluded by PLIP SO4.22: 9 residues within 4Å: Chain C: E.223, D.224, H.249, G.280, H.323, R.339 Ligands: AU.19, AU.20, EDO.23 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain D: A.54, M.57, E.58 Ligand excluded by PLIP SO4.27: 8 residues within 4Å: Chain D: A.6, E.7, K.10, T.85, T.90 Chain F: S.465 Chain I: F.568, F.570 Ligand excluded by PLIP SO4.30: 2 residues within 4Å: Chain E: I.26, R.27 Ligand excluded by PLIP SO4.31: 2 residues within 4Å: Chain E: L.108, R.112 Ligand excluded by PLIP SO4.41: 4 residues within 4Å: Chain F: Y.35, Y.83, I.97, E.429 Ligand excluded by PLIP SO4.42: 2 residues within 4Å: Chain F: I.500, Q.501 Ligand excluded by PLIP SO4.46: 9 residues within 4Å: Chain F: E.223, D.224, H.249, G.280, H.323, R.339 Ligands: AU.43, AU.44, EDO.47 Ligand excluded by PLIP SO4.50: 3 residues within 4Å: Chain G: A.54, M.57, E.58 Ligand excluded by PLIP SO4.51: 8 residues within 4Å: Chain C: F.568, F.570 Chain G: A.6, E.7, K.10, T.85, T.90 Chain I: S.465 Ligand excluded by PLIP SO4.54: 2 residues within 4Å: Chain H: I.26, R.27 Ligand excluded by PLIP SO4.55: 2 residues within 4Å: Chain H: L.108, R.112 Ligand excluded by PLIP SO4.65: 4 residues within 4Å: Chain I: Y.35, Y.83, I.97, E.429 Ligand excluded by PLIP SO4.66: 2 residues within 4Å: Chain I: I.500, Q.501 Ligand excluded by PLIP SO4.70: 9 residues within 4Å: Chain I: E.223, D.224, H.249, G.280, H.323, R.339 Ligands: AU.67, AU.68, EDO.71 Ligand excluded by PLIP

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

NI.8: 7 residues within 4Å: Chain C: K.220, H.222, H.249, H.275, G.280 Ligands: NI.9, OH.10 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.5, OH.10 NI.9: 6 residues within 4Å: Chain C: H.137, H.139, K.220, D.363 Ligands: NI.8, OH.10 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.7, OH.10 NI.32: 7 residues within 4Å: Chain F: K.220, H.222, H.249, H.275, G.280 Ligands: NI.33, OH.34 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.18, OH.34 NI.33: 6 residues within 4Å: Chain F: H.137, H.139, K.220, D.363 Ligands: NI.32, OH.34 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.20, OH.34 NI.56: 7 residues within 4Å: Chain I: K.220, H.222, H.249, H.275, G.280 Ligands: NI.57, OH.58 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.30, OH.58 NI.57: 6 residues within 4Å: Chain I: H.137, H.139, K.220, D.363 Ligands: NI.56, OH.58 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.33, OH.58

3 x OH: HYDROXIDE ION(Non-covalent)

OH.10: 8 residues within 4Å: Chain C: H.137, K.220, H.249, H.275, G.280, D.363 Ligands: NI.8, NI.9 No protein-ligand interaction detected (PLIP) OH.34: 8 residues within 4Å: Chain F: H.137, K.220, H.249, H.275, G.280, D.363 Ligands: NI.32, NI.33 No protein-ligand interaction detected (PLIP) OH.58: 8 residues within 4Å: Chain I: H.137, K.220, H.249, H.275, G.280, D.363 Ligands: NI.56, NI.57 No protein-ligand interaction detected (PLIP)

9 x AU: GOLD ION(Non-covalent)

AU.19: 5 residues within 4Å: Chain C: L.319, C.322, H.323 Ligands: AU.20, SO4.22 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:C.322, C:H.323 AU.20: 4 residues within 4Å: Chain C: C.322, M.367 Ligands: AU.19, SO4.22 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:C.322 AU.21: 3 residues within 4Å: Chain C: Q.387, T.554, C.555 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:C.555 AU.43: 5 residues within 4Å: Chain F: L.319, C.322, H.323 Ligands: AU.44, SO4.46 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:C.322, F:H.323 AU.44: 4 residues within 4Å: Chain F: C.322, M.367 Ligands: AU.43, SO4.46 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:C.322 AU.45: 3 residues within 4Å: Chain F: Q.387, T.554, C.555 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:C.555 AU.67: 5 residues within 4Å: Chain I: L.319, C.322, H.323 Ligands: AU.68, SO4.70 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:C.322, I:H.323 AU.68: 4 residues within 4Å: Chain I: C.322, M.367 Ligands: AU.67, SO4.70 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:C.322 AU.69: 3 residues within 4Å: Chain I: Q.387, T.554, C.555 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:C.555

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mazzei, L. et al., Inhibition Mechanism of Urease by Au(III) Compounds Unveiled by X-ray Diffraction Analysis. Acs Med.Chem.Lett. (2019)

Release Date

2019-05-01

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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