SMTL ID : 7p7n.1

X-RAY CRYSTAL STRUCTURE OF SPOROSARCINA PASTEURII UREASE INHIBITED BY THE GOLD(I)-PHOSPHINE COMPOUND Au(PEt3)I DETERMINED AT 1.80 ANGSTROMS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-3-3-3-mer

Ligands

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

EDO.1: 6 residues within 4Å: Chain A: K.24, G.27, L.28, K.29, D.67, D.68 Ligand excluded by PLIP EDO.2: 3 residues within 4Å: Chain A: F.42, E.59, H.62 Ligand excluded by PLIP EDO.3: 8 residues within 4Å: Chain A: M.1 Chain D: Y.32, V.36, M.76, I.77, D.78, D.79 Chain F: K.441 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: N.4, A.6, E.7, K.10 Chain F: F.568, F.570 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain B: S.67, G.68 Chain C: Y.12, N.43, K.48 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain B: G.88, N.89 Chain C: P.103, M.106, D.107, G.108, V.109 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain C: E.10, E.125, G.126 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain C: P.143, G.189, P.191, R.478 Ligand excluded by PLIP EDO.14: 7 residues within 4Å: Chain C: L.259, D.286, A.289, I.537, D.538, I.539 Chain H: R.34 Ligand excluded by PLIP EDO.34: 2 residues within 4Å: Chain C: Y.60, E.64 Ligand excluded by PLIP EDO.35: 4 residues within 4Å: Chain C: K.497, S.498, Q.501 Ligands: EDO.36 Ligand excluded by PLIP EDO.36: 4 residues within 4Å: Chain C: E.241, A.242, K.497 Ligands: EDO.35 Ligand excluded by PLIP EDO.37: 6 residues within 4Å: Chain C: Y.93, E.423, I.492, R.513, I.514 Ligands: SO4.33 Ligand excluded by PLIP EDO.38: 6 residues within 4Å: Chain D: K.24, G.27, L.28, K.29, D.67, D.68 Ligand excluded by PLIP EDO.39: 3 residues within 4Å: Chain D: F.42, E.59, H.62 Ligand excluded by PLIP EDO.40: 8 residues within 4Å: Chain D: M.1 Chain G: Y.32, V.36, M.76, I.77, D.78, D.79 Chain I: K.441 Ligand excluded by PLIP EDO.41: 6 residues within 4Å: Chain D: N.4, A.6, E.7, K.10 Chain I: F.568, F.570 Ligand excluded by PLIP EDO.42: 5 residues within 4Å: Chain E: S.67, G.68 Chain F: Y.12, N.43, K.48 Ligand excluded by PLIP EDO.47: 7 residues within 4Å: Chain E: G.88, N.89 Chain F: P.103, M.106, D.107, G.108, V.109 Ligand excluded by PLIP EDO.48: 3 residues within 4Å: Chain F: E.10, E.125, G.126 Ligand excluded by PLIP EDO.50: 4 residues within 4Å: Chain F: P.143, G.189, P.191, R.478 Ligand excluded by PLIP EDO.51: 7 residues within 4Å: Chain B: R.34 Chain F: L.259, D.286, A.289, I.537, D.538, I.539 Ligand excluded by PLIP EDO.71: 2 residues within 4Å: Chain F: Y.60, E.64 Ligand excluded by PLIP EDO.72: 4 residues within 4Å: Chain F: K.497, S.498, Q.501 Ligands: EDO.73 Ligand excluded by PLIP EDO.73: 4 residues within 4Å: Chain F: E.241, A.242, K.497 Ligands: EDO.72 Ligand excluded by PLIP EDO.74: 6 residues within 4Å: Chain F: Y.93, E.423, I.492, R.513, I.514 Ligands: SO4.70 Ligand excluded by PLIP EDO.75: 6 residues within 4Å: Chain G: K.24, G.27, L.28, K.29, D.67, D.68 Ligand excluded by PLIP EDO.76: 3 residues within 4Å: Chain G: F.42, E.59, H.62 Ligand excluded by PLIP EDO.77: 8 residues within 4Å: Chain A: Y.32, V.36, M.76, I.77, D.78, D.79 Chain C: K.441 Chain G: M.1 Ligand excluded by PLIP EDO.78: 6 residues within 4Å: Chain C: F.568, F.570 Chain G: N.4, A.6, E.7, K.10 Ligand excluded by PLIP EDO.79: 5 residues within 4Å: Chain H: S.67, G.68 Chain I: Y.12, N.43, K.48 Ligand excluded by PLIP EDO.84: 7 residues within 4Å: Chain H: G.88, N.89 Chain I: P.103, M.106, D.107, G.108, V.109 Ligand excluded by PLIP EDO.85: 3 residues within 4Å: Chain I: E.10, E.125, G.126 Ligand excluded by PLIP EDO.87: 4 residues within 4Å: Chain I: P.143, G.189, P.191, R.478 Ligand excluded by PLIP EDO.88: 7 residues within 4Å: Chain E: R.34 Chain I: L.259, D.286, A.289, I.537, D.538, I.539 Ligand excluded by PLIP EDO.108: 2 residues within 4Å: Chain I: Y.60, E.64 Ligand excluded by PLIP EDO.109: 4 residues within 4Å: Chain I: K.497, S.498, Q.501 Ligands: EDO.110 Ligand excluded by PLIP EDO.110: 4 residues within 4Å: Chain I: E.241, A.242, K.497 Ligands: EDO.109 Ligand excluded by PLIP EDO.111: 6 residues within 4Å: Chain I: Y.93, E.423, I.492, R.513, I.514 Ligands: SO4.107 Ligand excluded by PLIP

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

SO4.6: 3 residues within 4Å: Chain B: T.25, I.26, R.27 Ligand excluded by PLIP SO4.7: 2 residues within 4Å: Chain B: L.108, R.112 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain C: D.34, T.36, Y.38 Ligand excluded by PLIP SO4.22: 4 residues within 4Å: Chain C: Y.35, Y.83, I.97, E.429 Ligand excluded by PLIP SO4.23: 1 residues within 4Å: Ligands: SO4.31 Ligand excluded by PLIP SO4.24: 8 residues within 4Å: Chain C: H.222, E.223, D.224, H.249, G.280, R.339 Ligands: AU.19, AU.20 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain C: V.558, K.559, E.560 Ligand excluded by PLIP SO4.26: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.27: 4 residues within 4Å: Chain C: Y.93, H.422, E.423, G.430 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain C: C.322 Chain I: G.45, G.46, K.48 Ligand excluded by PLIP SO4.29: 6 residues within 4Å: Chain B: P.66, T.69 Chain C: I.3, Q.7, S.11, Y.12 Ligand excluded by PLIP SO4.30: 3 residues within 4Å: Chain C: K.33, D.34, Y.35 Ligand excluded by PLIP SO4.31: 5 residues within 4Å: Chain C: Y.60, E.64, N.65, I.114 Ligands: SO4.23 Ligand excluded by PLIP SO4.32: 5 residues within 4Å: Chain C: K.511 Chain F: K.511 Chain I: K.511 Ligands: SO4.69, SO4.106 Ligand excluded by PLIP SO4.33: 3 residues within 4Å: Chain C: R.513, I.514 Ligands: EDO.37 Ligand excluded by PLIP SO4.43: 3 residues within 4Å: Chain E: T.25, I.26, R.27 Ligand excluded by PLIP SO4.44: 2 residues within 4Å: Chain E: L.108, R.112 Ligand excluded by PLIP SO4.58: 3 residues within 4Å: Chain F: D.34, T.36, Y.38 Ligand excluded by PLIP SO4.59: 4 residues within 4Å: Chain F: Y.35, Y.83, I.97, E.429 Ligand excluded by PLIP SO4.60: 1 residues within 4Å: Ligands: SO4.68 Ligand excluded by PLIP SO4.61: 8 residues within 4Å: Chain F: H.222, E.223, D.224, H.249, G.280, R.339 Ligands: AU.56, AU.57 Ligand excluded by PLIP SO4.62: 3 residues within 4Å: Chain F: V.558, K.559, E.560 Ligand excluded by PLIP SO4.63: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.64: 4 residues within 4Å: Chain F: Y.93, H.422, E.423, G.430 Ligand excluded by PLIP SO4.65: 4 residues within 4Å: Chain C: G.45, G.46, K.48 Chain F: C.322 Ligand excluded by PLIP SO4.66: 6 residues within 4Å: Chain E: P.66, T.69 Chain F: I.3, Q.7, S.11, Y.12 Ligand excluded by PLIP SO4.67: 3 residues within 4Å: Chain F: K.33, D.34, Y.35 Ligand excluded by PLIP SO4.68: 5 residues within 4Å: Chain F: Y.60, E.64, N.65, I.114 Ligands: SO4.60 Ligand excluded by PLIP SO4.69: 5 residues within 4Å: Chain C: K.511 Chain F: K.511 Chain I: K.511 Ligands: SO4.32, SO4.106 Ligand excluded by PLIP SO4.70: 3 residues within 4Å: Chain F: R.513, I.514 Ligands: EDO.74 Ligand excluded by PLIP SO4.80: 3 residues within 4Å: Chain H: T.25, I.26, R.27 Ligand excluded by PLIP SO4.81: 2 residues within 4Å: Chain H: L.108, R.112 Ligand excluded by PLIP SO4.95: 3 residues within 4Å: Chain I: D.34, T.36, Y.38 Ligand excluded by PLIP SO4.96: 4 residues within 4Å: Chain I: Y.35, Y.83, I.97, E.429 Ligand excluded by PLIP SO4.97: 1 residues within 4Å: Ligands: SO4.105 Ligand excluded by PLIP SO4.98: 8 residues within 4Å: Chain I: H.222, E.223, D.224, H.249, G.280, R.339 Ligands: AU.93, AU.94 Ligand excluded by PLIP SO4.99: 3 residues within 4Å: Chain I: V.558, K.559, E.560 Ligand excluded by PLIP SO4.100: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.101: 4 residues within 4Å: Chain I: Y.93, H.422, E.423, G.430 Ligand excluded by PLIP SO4.102: 4 residues within 4Å: Chain F: G.45, G.46, K.48 Chain I: C.322 Ligand excluded by PLIP SO4.103: 6 residues within 4Å: Chain H: P.66, T.69 Chain I: I.3, Q.7, S.11, Y.12 Ligand excluded by PLIP SO4.104: 3 residues within 4Å: Chain I: K.33, D.34, Y.35 Ligand excluded by PLIP SO4.105: 5 residues within 4Å: Chain I: Y.60, E.64, N.65, I.114 Ligands: SO4.97 Ligand excluded by PLIP SO4.106: 5 residues within 4Å: Chain C: K.511 Chain F: K.511 Chain I: K.511 Ligands: SO4.32, SO4.69 Ligand excluded by PLIP SO4.107: 3 residues within 4Å: Chain I: R.513, I.514 Ligands: EDO.111 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, O.12 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.7, O.12 NI.9: 6 residues within 4Å: Chain C: H.137, H.139, K.220, D.363 Ligands: NI.8, O.12 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, O.12 NI.45: 7 residues within 4Å: Chain F: K.220, H.222, H.249, H.275, G.280 Ligands: NI.46, O.49 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.28, O.49 NI.46: 6 residues within 4Å: Chain F: H.137, H.139, K.220, D.363 Ligands: NI.45, O.49 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, O.49 NI.82: 7 residues within 4Å: Chain I: K.220, H.222, H.249, H.275, G.280 Ligands: NI.83, O.86 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.49, O.86 NI.83: 6 residues within 4Å: Chain I: H.137, H.139, K.220, D.363 Ligands: NI.82, O.86 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.49, O.86

3 x O: OXYGEN ATOM(Non-covalent)

O.12: 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) O.49: 8 residues within 4Å: Chain F: H.137, K.220, H.249, H.275, G.280, D.363 Ligands: NI.45, NI.46 No protein-ligand interaction detected (PLIP) O.86: 8 residues within 4Å: Chain I: H.137, K.220, H.249, H.275, G.280, D.363 Ligands: NI.82, NI.83 No protein-ligand interaction detected (PLIP)

3 x AUF: triethylphosphanuidylgold(1+)(Non-covalent)

AUF.15: 4 residues within 4Å: Chain C: Q.387, T.554, C.555, E.556 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:C.555 AUF.52: 4 residues within 4Å: Chain F: Q.387, T.554, C.555, E.556 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:C.555 AUF.89: 4 residues within 4Å: Chain I: Q.387, T.554, C.555, E.556 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:C.555

15 x AU: GOLD ION(Non-covalent)(Non-functional Binders)

AU.16: 1 residues within 4Å: Chain C: M.367 No protein-ligand interaction detected (PLIP) AU.17: 1 residues within 4Å: Ligands: AU.18 No protein-ligand interaction detected (PLIP) AU.18: 1 residues within 4Å: Ligands: AU.17 No protein-ligand interaction detected (PLIP) AU.19: 5 residues within 4Å: Chain C: L.319, C.322, R.339 Ligands: AU.20, SO4.24 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:C.322 AU.20: 4 residues within 4Å: Chain C: V.321, C.322 Ligands: AU.19, SO4.24 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:C.322 AU.53: 1 residues within 4Å: Chain F: M.367 No protein-ligand interaction detected (PLIP) AU.54: 1 residues within 4Å: Ligands: AU.55 No protein-ligand interaction detected (PLIP) AU.55: 1 residues within 4Å: Ligands: AU.54 No protein-ligand interaction detected (PLIP) AU.56: 5 residues within 4Å: Chain F: L.319, C.322, R.339 Ligands: AU.57, SO4.61 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:C.322 AU.57: 4 residues within 4Å: Chain F: V.321, C.322 Ligands: AU.56, SO4.61 1 PLIP interactions: 1 interactions with chain F Metal complexes: F:C.322 AU.90: 1 residues within 4Å: Chain I: M.367 No protein-ligand interaction detected (PLIP) AU.91: 1 residues within 4Å: Ligands: AU.92 No protein-ligand interaction detected (PLIP) AU.92: 1 residues within 4Å: Ligands: AU.91 No protein-ligand interaction detected (PLIP) AU.93: 5 residues within 4Å: Chain I: L.319, C.322, R.339 Ligands: AU.94, SO4.98 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:C.322 AU.94: 4 residues within 4Å: Chain I: V.321, C.322 Ligands: AU.93, SO4.98 1 PLIP interactions: 1 interactions with chain I Metal complexes: I:C.322

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mazzei, L. et al., Medicinal Au(I) compounds targeting urease as prospective antimicrobial agents: unveiling the structural basis for enzyme inhibition. Dalton Trans (2021)

Release Date

2022-06-01

Peptides

Urease subunit gamma: ADG
Urease subunit beta: BEH
Urease subunit alpha: CFI

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

D
AAA

G
AAA

B
BBB

E
BBB

H
BBB

C
CCC

F
CCC

I
CCC

Urease subunit gamma

Urease subunit beta

Urease subunit alpha

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