SMTL ID : 6znz.1

1.89 A resolution 4-methylcatechol (4-methylbenzene-1,2-diol) inhibited Sporosarcina pasteurii urease

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 Å

Oligo State

hetero-3-3-3-mer

Ligands

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

EDO.1: 1 residues within 4Å: Chain A: N.97 Ligand excluded by PLIP EDO.2: 3 residues within 4Å: Chain A: F.42, E.59, H.62 Ligand excluded by PLIP EDO.3: 2 residues within 4Å: Chain A: H.62, T.65 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: M.1, H.2 Chain D: Y.32, I.77, D.79 Ligand excluded by PLIP EDO.5: 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.6: 6 residues within 4Å: Chain A: K.24, G.27, L.28, K.29, D.67, D.68 Ligand excluded by PLIP EDO.7: 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.9: 3 residues within 4Å: Chain B: I.65, V.81, E.82 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain B: Q.37 Chain C: G.46 Chain F: L.253, H.323, L.325, F.335 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain B: D.97 Chain F: P.229, D.233, A.265 Ligand excluded by PLIP EDO.18: 2 residues within 4Å: Chain C: Y.35 Ligands: EDO.24 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain B: S.67 Chain C: Y.12, N.43, K.48 Ligand excluded by PLIP EDO.20: 1 residues within 4Å: Chain C: K.2 Ligand excluded by PLIP EDO.21: 2 residues within 4Å: Chain C: D.107, G.108 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain C: K.185, K.507, L.508, G.509 Ligand excluded by PLIP EDO.23: 3 residues within 4Å: Chain C: Y.79, K.529, W.530 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain C: Y.35, Y.83, I.97, E.429 Ligands: EDO.18 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain C: E.10, E.125, G.126 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain C: T.36, T.37, Y.38 Ligands: EDO.27 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain C: D.34, T.36, Y.38 Ligands: EDO.26 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain C: Y.60, E.64, N.65, I.114 Ligands: SO4.37 Ligand excluded by PLIP EDO.29: 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.30: 3 residues within 4Å: Chain C: H.293, P.294, N.295 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain C: H.422, E.423, G.430 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain C: Y.93, E.423, R.513, I.514 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain C: T.516, K.518 Ligands: SO4.39 Ligand excluded by PLIP EDO.34: 6 residues within 4Å: Chain C: P.143, G.189, L.190, P.191, R.478 Chain I: V.483 Ligand excluded by PLIP EDO.40: 1 residues within 4Å: Chain D: N.97 Ligand excluded by PLIP EDO.41: 3 residues within 4Å: Chain D: F.42, E.59, H.62 Ligand excluded by PLIP EDO.42: 2 residues within 4Å: Chain D: H.62, T.65 Ligand excluded by PLIP EDO.43: 5 residues within 4Å: Chain D: M.1, H.2 Chain G: Y.32, I.77, D.79 Ligand excluded by PLIP EDO.44: 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.45: 6 residues within 4Å: Chain D: K.24, G.27, L.28, K.29, D.67, D.68 Ligand excluded by PLIP EDO.46: 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.48: 3 residues within 4Å: Chain E: I.65, V.81, E.82 Ligand excluded by PLIP EDO.49: 6 residues within 4Å: Chain E: Q.37 Chain F: G.46 Chain I: L.253, H.323, L.325, F.335 Ligand excluded by PLIP EDO.50: 4 residues within 4Å: Chain E: D.97 Chain I: P.229, D.233, A.265 Ligand excluded by PLIP EDO.57: 2 residues within 4Å: Chain F: Y.35 Ligands: EDO.63 Ligand excluded by PLIP EDO.58: 4 residues within 4Å: Chain E: S.67 Chain F: Y.12, N.43, K.48 Ligand excluded by PLIP EDO.59: 1 residues within 4Å: Chain F: K.2 Ligand excluded by PLIP EDO.60: 2 residues within 4Å: Chain F: D.107, G.108 Ligand excluded by PLIP EDO.61: 4 residues within 4Å: Chain F: K.185, K.507, L.508, G.509 Ligand excluded by PLIP EDO.62: 3 residues within 4Å: Chain F: Y.79, K.529, W.530 Ligand excluded by PLIP EDO.63: 5 residues within 4Å: Chain F: Y.35, Y.83, I.97, E.429 Ligands: EDO.57 Ligand excluded by PLIP EDO.64: 3 residues within 4Å: Chain F: E.10, E.125, G.126 Ligand excluded by PLIP EDO.65: 4 residues within 4Å: Chain F: T.36, T.37, Y.38 Ligands: EDO.66 Ligand excluded by PLIP EDO.66: 4 residues within 4Å: Chain F: D.34, T.36, Y.38 Ligands: EDO.65 Ligand excluded by PLIP EDO.67: 5 residues within 4Å: Chain F: Y.60, E.64, N.65, I.114 Ligands: SO4.76 Ligand excluded by PLIP EDO.68: 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.69: 3 residues within 4Å: Chain F: H.293, P.294, N.295 Ligand excluded by PLIP EDO.70: 3 residues within 4Å: Chain F: H.422, E.423, G.430 Ligand excluded by PLIP EDO.71: 4 residues within 4Å: Chain F: Y.93, E.423, R.513, I.514 Ligand excluded by PLIP EDO.72: 3 residues within 4Å: Chain F: T.516, K.518 Ligands: SO4.78 Ligand excluded by PLIP EDO.73: 6 residues within 4Å: Chain C: V.483 Chain F: P.143, G.189, L.190, P.191, R.478 Ligand excluded by PLIP EDO.79: 1 residues within 4Å: Chain G: N.97 Ligand excluded by PLIP EDO.80: 3 residues within 4Å: Chain G: F.42, E.59, H.62 Ligand excluded by PLIP EDO.81: 2 residues within 4Å: Chain G: H.62, T.65 Ligand excluded by PLIP EDO.82: 5 residues within 4Å: Chain A: Y.32, I.77, D.79 Chain G: M.1, H.2 Ligand excluded by PLIP EDO.83: 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.84: 6 residues within 4Å: Chain G: K.24, G.27, L.28, K.29, D.67, D.68 Ligand excluded by PLIP EDO.85: 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.87: 3 residues within 4Å: Chain H: I.65, V.81, E.82 Ligand excluded by PLIP EDO.88: 6 residues within 4Å: Chain C: L.253, H.323, L.325, F.335 Chain H: Q.37 Chain I: G.46 Ligand excluded by PLIP EDO.89: 4 residues within 4Å: Chain C: P.229, D.233, A.265 Chain H: D.97 Ligand excluded by PLIP EDO.96: 2 residues within 4Å: Chain I: Y.35 Ligands: EDO.102 Ligand excluded by PLIP EDO.97: 4 residues within 4Å: Chain H: S.67 Chain I: Y.12, N.43, K.48 Ligand excluded by PLIP EDO.98: 1 residues within 4Å: Chain I: K.2 Ligand excluded by PLIP EDO.99: 2 residues within 4Å: Chain I: D.107, G.108 Ligand excluded by PLIP EDO.100: 4 residues within 4Å: Chain I: K.185, K.507, L.508, G.509 Ligand excluded by PLIP EDO.101: 3 residues within 4Å: Chain I: Y.79, K.529, W.530 Ligand excluded by PLIP EDO.102: 5 residues within 4Å: Chain I: Y.35, Y.83, I.97, E.429 Ligands: EDO.96 Ligand excluded by PLIP EDO.103: 3 residues within 4Å: Chain I: E.10, E.125, G.126 Ligand excluded by PLIP EDO.104: 4 residues within 4Å: Chain I: T.36, T.37, Y.38 Ligands: EDO.105 Ligand excluded by PLIP EDO.105: 4 residues within 4Å: Chain I: D.34, T.36, Y.38 Ligands: EDO.104 Ligand excluded by PLIP EDO.106: 5 residues within 4Å: Chain I: Y.60, E.64, N.65, I.114 Ligands: SO4.115 Ligand excluded by PLIP EDO.107: 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.108: 3 residues within 4Å: Chain I: H.293, P.294, N.295 Ligand excluded by PLIP EDO.109: 3 residues within 4Å: Chain I: H.422, E.423, G.430 Ligand excluded by PLIP EDO.110: 4 residues within 4Å: Chain I: Y.93, E.423, R.513, I.514 Ligand excluded by PLIP EDO.111: 3 residues within 4Å: Chain I: T.516, K.518 Ligands: SO4.117 Ligand excluded by PLIP EDO.112: 6 residues within 4Å: Chain F: V.483 Chain I: P.143, G.189, L.190, P.191, R.478 Ligand excluded by PLIP

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

SO4.8: 3 residues within 4Å: Chain A: M.70, E.71 Chain C: R.566 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain B: T.25, I.26, R.27 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain B: G.101, S.102, N.105 Ligand excluded by PLIP SO4.14: 2 residues within 4Å: Chain B: L.108, R.112 Ligand excluded by PLIP SO4.35: 5 residues within 4Å: Chain C: K.511 Chain F: K.511 Chain I: K.511 Ligands: SO4.74, SO4.113 Ligand excluded by PLIP SO4.36: 3 residues within 4Å: Chain C: V.558, K.559, E.560 Ligand excluded by PLIP SO4.37: 2 residues within 4Å: Chain C: N.65 Ligands: EDO.28 Ligand excluded by PLIP SO4.38: 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 SO4.39: 2 residues within 4Å: Chain C: K.518 Ligands: EDO.33 Ligand excluded by PLIP SO4.47: 3 residues within 4Å: Chain D: M.70, E.71 Chain F: R.566 Ligand excluded by PLIP SO4.51: 3 residues within 4Å: Chain E: T.25, I.26, R.27 Ligand excluded by PLIP SO4.52: 3 residues within 4Å: Chain E: G.101, S.102, N.105 Ligand excluded by PLIP SO4.53: 2 residues within 4Å: Chain E: L.108, R.112 Ligand excluded by PLIP SO4.74: 5 residues within 4Å: Chain C: K.511 Chain F: K.511 Chain I: K.511 Ligands: SO4.35, SO4.113 Ligand excluded by PLIP SO4.75: 3 residues within 4Å: Chain F: V.558, K.559, E.560 Ligand excluded by PLIP SO4.76: 2 residues within 4Å: Chain F: N.65 Ligands: EDO.67 Ligand excluded by PLIP SO4.77: 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 SO4.78: 2 residues within 4Å: Chain F: K.518 Ligands: EDO.72 Ligand excluded by PLIP SO4.86: 3 residues within 4Å: Chain G: M.70, E.71 Chain I: R.566 Ligand excluded by PLIP SO4.90: 3 residues within 4Å: Chain H: T.25, I.26, R.27 Ligand excluded by PLIP SO4.91: 3 residues within 4Å: Chain H: G.101, S.102, N.105 Ligand excluded by PLIP SO4.92: 2 residues within 4Å: Chain H: L.108, R.112 Ligand excluded by PLIP SO4.113: 5 residues within 4Å: Chain C: K.511 Chain F: K.511 Chain I: K.511 Ligands: SO4.35, SO4.74 Ligand excluded by PLIP SO4.114: 3 residues within 4Å: Chain I: V.558, K.559, E.560 Ligand excluded by PLIP SO4.115: 2 residues within 4Å: Chain I: N.65 Ligands: EDO.106 Ligand excluded by PLIP SO4.116: 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 SO4.117: 2 residues within 4Å: Chain I: K.518 Ligands: EDO.111 Ligand excluded by PLIP

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

NI.15: 8 residues within 4Å: Chain C: H.137, K.220, H.222, H.249, H.275, G.280 Ligands: NI.16, OH.17 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, OH.17 NI.16: 6 residues within 4Å: Chain C: H.137, H.139, K.220, D.363 Ligands: NI.15, OH.17 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.17 NI.54: 8 residues within 4Å: Chain F: H.137, K.220, H.222, H.249, H.275, G.280 Ligands: NI.55, OH.56 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.30, OH.56 NI.55: 6 residues within 4Å: Chain F: H.137, H.139, K.220, D.363 Ligands: NI.54, OH.56 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.30, OH.56 NI.93: 8 residues within 4Å: Chain I: H.137, K.220, H.222, H.249, H.275, G.280 Ligands: NI.94, OH.95 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.52, OH.95 NI.94: 6 residues within 4Å: Chain I: H.137, H.139, K.220, D.363 Ligands: NI.93, OH.95 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.52, OH.95

3 x OH: HYDROXIDE ION(Non-covalent)

OH.17: 8 residues within 4Å: Chain C: H.137, K.220, H.249, H.275, G.280, D.363 Ligands: NI.15, NI.16 No protein-ligand interaction detected (PLIP) OH.56: 8 residues within 4Å: Chain F: H.137, K.220, H.249, H.275, G.280, D.363 Ligands: NI.54, NI.55 No protein-ligand interaction detected (PLIP) OH.95: 8 residues within 4Å: Chain I: H.137, K.220, H.249, H.275, G.280, D.363 Ligands: NI.93, NI.94 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mazzei, L. et al., Inhibition of Urease, a Ni-Enzyme: The Reactivity of a Key Thiol With Mono- and Di-Substituted Catechols Elucidated by Kinetic, Structural, and Theoretical Studies. Angew.Chem.Int.Ed.Engl. (2021)

Release Date

2020-12-23

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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