SMTL ID : 7b59.1

X-ray crystal structure of Sporosarcina pasteurii urease inhibited by Ag(PEt3)Br determined at 1.63 Angstroms

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

hetero-3-3-3-mer

Ligands

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

EDO.1: 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.2: 9 residues within 4Å: Chain A: G.50, K.51, T.52, F.86, P.87, D.88 Chain F: V.309, N.310, K.559 Ligand excluded by PLIP EDO.3: 3 residues within 4Å: Chain A: M.70, E.71 Chain C: R.566 Ligand excluded by PLIP EDO.4: 8 residues within 4Å: Chain A: Y.32, V.36, M.76, I.77, D.79, I.80 Chain C: Q.472 Chain G: M.1 Ligand excluded by PLIP EDO.6: 4 residues within 4Å: Chain B: R.27, E.78, M.79, E.80 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain B: D.97 Chain F: P.229, D.233, A.265 Ligand excluded by PLIP EDO.8: 2 residues within 4Å: Chain B: N.89, E.91 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain B: T.25, E.80, V.81, E.82 Ligands: SO4.11 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain B: S.67, G.68 Chain C: S.11, Y.12, N.43, K.48 Ligand excluded by PLIP EDO.17: 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.19: 7 residues within 4Å: Chain C: D.224, C.322, H.323 Chain I: G.45, G.46 Ligands: AG.22, SO4.31 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain C: L.253, H.323, L.325, D.332, F.335 Chain H: Q.37 Chain I: G.46 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain C: T.516, K.518 Ligands: SO4.33 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain C: Y.93, E.423, I.492, R.513, I.514, G.515 Ligands: SO4.34 Ligand excluded by PLIP EDO.38: 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.39: 9 residues within 4Å: Chain D: 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.40: 3 residues within 4Å: Chain D: M.70, E.71 Chain F: R.566 Ligand excluded by PLIP EDO.41: 8 residues within 4Å: Chain A: M.1 Chain D: Y.32, V.36, M.76, I.77, D.79, I.80 Chain F: Q.472 Ligand excluded by PLIP EDO.43: 4 residues within 4Å: Chain E: R.27, E.78, M.79, E.80 Ligand excluded by PLIP EDO.44: 4 residues within 4Å: Chain E: D.97 Chain I: P.229, D.233, A.265 Ligand excluded by PLIP EDO.45: 2 residues within 4Å: Chain E: N.89, E.91 Ligand excluded by PLIP EDO.46: 5 residues within 4Å: Chain E: T.25, E.80, V.81, E.82 Ligands: SO4.48 Ligand excluded by PLIP EDO.53: 6 residues within 4Å: Chain E: S.67, G.68 Chain F: S.11, Y.12, N.43, K.48 Ligand excluded by PLIP EDO.54: 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.56: 7 residues within 4Å: Chain C: G.45, G.46 Chain F: D.224, C.322, H.323 Ligands: AG.59, SO4.68 Ligand excluded by PLIP EDO.57: 7 residues within 4Å: Chain B: Q.37 Chain C: G.46 Chain F: L.253, H.323, L.325, D.332, F.335 Ligand excluded by PLIP EDO.60: 3 residues within 4Å: Chain F: T.516, K.518 Ligands: SO4.70 Ligand excluded by PLIP EDO.61: 7 residues within 4Å: Chain F: Y.93, E.423, I.492, R.513, I.514, G.515 Ligands: SO4.71 Ligand excluded by PLIP EDO.75: 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.76: 9 residues within 4Å: Chain C: 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.77: 3 residues within 4Å: Chain G: M.70, E.71 Chain I: R.566 Ligand excluded by PLIP EDO.78: 8 residues within 4Å: Chain D: M.1 Chain G: Y.32, V.36, M.76, I.77, D.79, I.80 Chain I: Q.472 Ligand excluded by PLIP EDO.80: 4 residues within 4Å: Chain H: R.27, E.78, M.79, E.80 Ligand excluded by PLIP EDO.81: 4 residues within 4Å: Chain C: P.229, D.233, A.265 Chain H: D.97 Ligand excluded by PLIP EDO.82: 2 residues within 4Å: Chain H: N.89, E.91 Ligand excluded by PLIP EDO.83: 5 residues within 4Å: Chain H: T.25, E.80, V.81, E.82 Ligands: SO4.85 Ligand excluded by PLIP EDO.90: 6 residues within 4Å: Chain H: S.67, G.68 Chain I: S.11, Y.12, N.43, K.48 Ligand excluded by PLIP EDO.91: 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.93: 7 residues within 4Å: Chain F: G.45, G.46 Chain I: D.224, C.322, H.323 Ligands: AG.96, SO4.105 Ligand excluded by PLIP EDO.94: 7 residues within 4Å: Chain E: Q.37 Chain F: G.46 Chain I: L.253, H.323, L.325, D.332, F.335 Ligand excluded by PLIP EDO.97: 3 residues within 4Å: Chain I: T.516, K.518 Ligands: SO4.107 Ligand excluded by PLIP EDO.98: 7 residues within 4Å: Chain I: Y.93, E.423, I.492, R.513, I.514, G.515 Ligands: SO4.108 Ligand excluded by PLIP

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

SO4.5: 11 residues within 4Å: Chain A: F.14, L.15, E.18 Chain D: F.14, L.15, E.18 Chain G: F.14, L.15, E.18 Ligands: SO4.42, SO4.79 Ligand excluded by PLIP SO4.10: 3 residues within 4Å: Chain B: T.25, I.26, R.27 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain B: M.79, E.80 Ligands: EDO.9 Ligand excluded by PLIP SO4.12: 2 residues within 4Å: Chain B: L.108, R.112 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain B: G.101, S.102, N.105 Ligand excluded by PLIP SO4.25: 4 residues within 4Å: Chain C: Y.35, Y.83, I.97, E.429 Ligand excluded by PLIP SO4.26: 2 residues within 4Å: Chain C: S.204, I.205 Ligand excluded by PLIP SO4.27: 3 residues within 4Å: Chain C: H.293, P.294, N.295 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain C: K.386, V.558, K.559, E.560 Ligand excluded by PLIP SO4.29: 4 residues within 4Å: Chain C: Y.93, H.422, E.423, G.430 Ligand excluded by PLIP SO4.30: 4 residues within 4Å: Chain C: E.343, E.542, T.543, Y.544 Ligand excluded by PLIP SO4.31: 12 residues within 4Å: Chain C: A.170, H.222, E.223, H.249, G.280, C.322, H.323, R.339, M.367 Ligands: EDO.19, AG.21, AG.22 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: 2 residues within 4Å: Chain C: K.518 Ligands: EDO.23 Ligand excluded by PLIP SO4.34: 3 residues within 4Å: Chain C: R.513, I.514 Ligands: EDO.24 Ligand excluded by PLIP SO4.35: 4 residues within 4Å: Chain C: V.16, D.34, T.36, Y.38 Ligand excluded by PLIP SO4.36: 2 residues within 4Å: Chain C: D.34, Y.35 Ligand excluded by PLIP SO4.37: 4 residues within 4Å: Chain C: Y.60, E.64, N.65, I.114 Ligand excluded by PLIP SO4.42: 11 residues within 4Å: Chain A: F.14, L.15, E.18 Chain D: F.14, L.15, E.18 Chain G: F.14, L.15, E.18 Ligands: SO4.5, SO4.79 Ligand excluded by PLIP SO4.47: 3 residues within 4Å: Chain E: T.25, I.26, R.27 Ligand excluded by PLIP SO4.48: 3 residues within 4Å: Chain E: M.79, E.80 Ligands: EDO.46 Ligand excluded by PLIP SO4.49: 2 residues within 4Å: Chain E: L.108, R.112 Ligand excluded by PLIP SO4.50: 3 residues within 4Å: Chain E: G.101, S.102, N.105 Ligand excluded by PLIP SO4.62: 4 residues within 4Å: Chain F: Y.35, Y.83, I.97, E.429 Ligand excluded by PLIP SO4.63: 2 residues within 4Å: Chain F: S.204, I.205 Ligand excluded by PLIP SO4.64: 3 residues within 4Å: Chain F: H.293, P.294, N.295 Ligand excluded by PLIP SO4.65: 4 residues within 4Å: Chain F: K.386, V.558, K.559, E.560 Ligand excluded by PLIP SO4.66: 4 residues within 4Å: Chain F: Y.93, H.422, E.423, G.430 Ligand excluded by PLIP SO4.67: 4 residues within 4Å: Chain F: E.343, E.542, T.543, Y.544 Ligand excluded by PLIP SO4.68: 12 residues within 4Å: Chain F: A.170, H.222, E.223, H.249, G.280, C.322, H.323, R.339, M.367 Ligands: EDO.56, AG.58, AG.59 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: 2 residues within 4Å: Chain F: K.518 Ligands: EDO.60 Ligand excluded by PLIP SO4.71: 3 residues within 4Å: Chain F: R.513, I.514 Ligands: EDO.61 Ligand excluded by PLIP SO4.72: 4 residues within 4Å: Chain F: V.16, D.34, T.36, Y.38 Ligand excluded by PLIP SO4.73: 2 residues within 4Å: Chain F: D.34, Y.35 Ligand excluded by PLIP SO4.74: 4 residues within 4Å: Chain F: Y.60, E.64, N.65, I.114 Ligand excluded by PLIP SO4.79: 11 residues within 4Å: Chain A: F.14, L.15, E.18 Chain D: F.14, L.15, E.18 Chain G: F.14, L.15, E.18 Ligands: SO4.5, SO4.42 Ligand excluded by PLIP SO4.84: 3 residues within 4Å: Chain H: T.25, I.26, R.27 Ligand excluded by PLIP SO4.85: 3 residues within 4Å: Chain H: M.79, E.80 Ligands: EDO.83 Ligand excluded by PLIP SO4.86: 2 residues within 4Å: Chain H: L.108, R.112 Ligand excluded by PLIP SO4.87: 3 residues within 4Å: Chain H: G.101, S.102, N.105 Ligand excluded by PLIP SO4.99: 4 residues within 4Å: Chain I: Y.35, Y.83, I.97, E.429 Ligand excluded by PLIP SO4.100: 2 residues within 4Å: Chain I: S.204, I.205 Ligand excluded by PLIP SO4.101: 3 residues within 4Å: Chain I: H.293, P.294, N.295 Ligand excluded by PLIP SO4.102: 4 residues within 4Å: Chain I: K.386, V.558, K.559, E.560 Ligand excluded by PLIP SO4.103: 4 residues within 4Å: Chain I: Y.93, H.422, E.423, G.430 Ligand excluded by PLIP SO4.104: 4 residues within 4Å: Chain I: E.343, E.542, T.543, Y.544 Ligand excluded by PLIP SO4.105: 12 residues within 4Å: Chain I: A.170, H.222, E.223, H.249, G.280, C.322, H.323, R.339, M.367 Ligands: EDO.93, AG.95, AG.96 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: 2 residues within 4Å: Chain I: K.518 Ligands: EDO.97 Ligand excluded by PLIP SO4.108: 3 residues within 4Å: Chain I: R.513, I.514 Ligands: EDO.98 Ligand excluded by PLIP SO4.109: 4 residues within 4Å: Chain I: V.16, D.34, T.36, Y.38 Ligand excluded by PLIP SO4.110: 2 residues within 4Å: Chain I: D.34, Y.35 Ligand excluded by PLIP SO4.111: 4 residues within 4Å: Chain I: Y.60, E.64, N.65, I.114 Ligand excluded by PLIP

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

NI.14: 7 residues within 4Å: Chain C: K.220, H.222, H.249, H.275, G.280 Ligands: NI.15, O.18 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.9, O.18 NI.15: 6 residues within 4Å: Chain C: H.137, H.139, K.220, D.363 Ligands: NI.14, O.18 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.9, O.18 NI.51: 7 residues within 4Å: Chain F: K.220, H.222, H.249, H.275, G.280 Ligands: NI.52, O.55 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.37, O.55 NI.52: 6 residues within 4Å: Chain F: H.137, H.139, K.220, D.363 Ligands: NI.51, O.55 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.37, O.55 NI.88: 7 residues within 4Å: Chain I: K.220, H.222, H.249, H.275, G.280 Ligands: NI.89, O.92 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.64, O.92 NI.89: 6 residues within 4Å: Chain I: H.137, H.139, K.220, D.363 Ligands: NI.88, O.92 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, O.92

3 x O: OXYGEN ATOM(Non-covalent)

O.18: 8 residues within 4Å: Chain C: H.137, K.220, H.249, H.275, G.280, D.363 Ligands: NI.14, NI.15 No protein-ligand interaction detected (PLIP) O.55: 8 residues within 4Å: Chain F: H.137, K.220, H.249, H.275, G.280, D.363 Ligands: NI.51, NI.52 No protein-ligand interaction detected (PLIP) O.92: 8 residues within 4Å: Chain I: H.137, K.220, H.249, H.275, G.280, D.363 Ligands: NI.88, NI.89 No protein-ligand interaction detected (PLIP)

6 x AG: SILVER ION(Non-covalent)

AG.21: 5 residues within 4Å: Chain C: C.322, R.339, M.367 Ligands: AG.22, SO4.31 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:C.322, H2O.23 AG.22: 5 residues within 4Å: Chain C: C.322, H.323 Ligands: EDO.19, AG.21, SO4.31 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:C.322, C:H.323 AG.58: 5 residues within 4Å: Chain F: C.322, R.339, M.367 Ligands: AG.59, SO4.68 2 PLIP interactions: 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:C.322, H2O.50 AG.59: 5 residues within 4Å: Chain F: C.322, H.323 Ligands: EDO.56, AG.58, SO4.68 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:C.322, F:H.323 AG.95: 5 residues within 4Å: Chain I: C.322, R.339, M.367 Ligands: AG.96, SO4.105 2 PLIP interactions: 1 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:C.322, H2O.77 AG.96: 5 residues within 4Å: Chain I: C.322, H.323 Ligands: EDO.93, AG.95, SO4.105 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:C.322, I:H.323

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mazzei, L. et al., Kinetic and structural analysis of the inactivation of urease by mixed-ligand phosphine halide Ag(I) complexes. J.Inorg.Biochem. (2021)

Release Date

2021-10-13

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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