SMTL ID : 5g4h.1

1.50 A resolution catechol (1,2-dihydroxybenzene) inhibited Sporosarcina pasteurii urease

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-3-3-3-mer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: M.70, E.71 Chain C: R.566 Ligand excluded by PLIP SO4.4: 1 residues within 4Å: Chain B: R.116 Ligand excluded by PLIP SO4.6: 2 residues within 4Å: Chain B: I.30, R.31 Ligand excluded by PLIP SO4.10: 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 SO4.12: 3 residues within 4Å: Chain C: V.558, K.559, E.560 Ligand excluded by PLIP SO4.25: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain D: M.70, E.71 Chain F: R.566 Ligand excluded by PLIP SO4.29: 1 residues within 4Å: Chain E: R.116 Ligand excluded by PLIP SO4.31: 2 residues within 4Å: Chain E: I.30, R.31 Ligand excluded by PLIP SO4.35: 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 SO4.37: 3 residues within 4Å: Chain F: V.558, K.559, E.560 Ligand excluded by PLIP SO4.50: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP SO4.51: 3 residues within 4Å: Chain G: M.70, E.71 Chain I: R.566 Ligand excluded by PLIP SO4.54: 1 residues within 4Å: Chain H: R.116 Ligand excluded by PLIP SO4.56: 2 residues within 4Å: Chain H: I.30, R.31 Ligand excluded by PLIP SO4.60: 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 SO4.62: 3 residues within 4Å: Chain I: V.558, K.559, E.560 Ligand excluded by PLIP SO4.75: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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

EDO.2: 6 residues within 4Å: Chain A: K.24, G.27, L.28, K.29, D.67, D.68 Ligand excluded by PLIP EDO.3: 4 residues within 4Å: Chain A: Y.32, I.77, D.79 Chain D: M.1 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain B: D.101 Chain I: P.229, D.233 Ligand excluded by PLIP EDO.13: 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.14: 4 residues within 4Å: Chain C: V.16, D.34, T.36, Y.38 Ligand excluded by PLIP EDO.15: 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.16: 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.17: 4 residues within 4Å: Chain B: S.71 Chain C: Y.12, N.43, K.48 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain C: Y.35, Y.83, I.97, E.429 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain C: F.568, F.570 Chain D: N.4, A.6, E.7, K.10 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain C: L.236, T.237, D.240, R.269 Ligand excluded by PLIP EDO.21: 3 residues within 4Å: Chain C: H.422, E.423, G.430 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain C: Y.93, E.423, R.513, I.514 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain C: P.143, G.189, P.191, R.478 Ligand excluded by PLIP EDO.24: 4 residues within 4Å: Chain C: P.177, W.178, E.181 Chain F: R.62 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain D: K.24, G.27, L.28, K.29, D.67, D.68 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain D: Y.32, I.77, D.79 Chain G: M.1 Ligand excluded by PLIP EDO.30: 3 residues within 4Å: Chain C: P.229, D.233 Chain E: D.101 Ligand excluded by PLIP EDO.38: 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.39: 4 residues within 4Å: Chain F: V.16, D.34, T.36, Y.38 Ligand excluded by PLIP EDO.40: 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.41: 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.42: 4 residues within 4Å: Chain E: S.71 Chain F: Y.12, N.43, K.48 Ligand excluded by PLIP EDO.43: 4 residues within 4Å: Chain F: Y.35, Y.83, I.97, E.429 Ligand excluded by PLIP EDO.44: 6 residues within 4Å: Chain F: F.568, F.570 Chain G: N.4, A.6, E.7, K.10 Ligand excluded by PLIP EDO.45: 4 residues within 4Å: Chain F: L.236, T.237, D.240, R.269 Ligand excluded by PLIP EDO.46: 3 residues within 4Å: Chain F: H.422, E.423, G.430 Ligand excluded by PLIP EDO.47: 4 residues within 4Å: Chain F: Y.93, E.423, R.513, I.514 Ligand excluded by PLIP EDO.48: 4 residues within 4Å: Chain F: P.143, G.189, P.191, R.478 Ligand excluded by PLIP EDO.49: 4 residues within 4Å: Chain F: P.177, W.178, E.181 Chain I: R.62 Ligand excluded by PLIP EDO.52: 6 residues within 4Å: Chain G: K.24, G.27, L.28, K.29, D.67, D.68 Ligand excluded by PLIP EDO.53: 4 residues within 4Å: Chain A: M.1 Chain G: Y.32, I.77, D.79 Ligand excluded by PLIP EDO.55: 3 residues within 4Å: Chain F: P.229, D.233 Chain H: D.101 Ligand excluded by PLIP EDO.63: 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.64: 4 residues within 4Å: Chain I: V.16, D.34, T.36, Y.38 Ligand excluded by PLIP EDO.65: 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.66: 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.67: 4 residues within 4Å: Chain H: S.71 Chain I: Y.12, N.43, K.48 Ligand excluded by PLIP EDO.68: 4 residues within 4Å: Chain I: Y.35, Y.83, I.97, E.429 Ligand excluded by PLIP EDO.69: 6 residues within 4Å: Chain A: N.4, A.6, E.7, K.10 Chain I: F.568, F.570 Ligand excluded by PLIP EDO.70: 4 residues within 4Å: Chain I: L.236, T.237, D.240, R.269 Ligand excluded by PLIP EDO.71: 3 residues within 4Å: Chain I: H.422, E.423, G.430 Ligand excluded by PLIP EDO.72: 4 residues within 4Å: Chain I: Y.93, E.423, R.513, I.514 Ligand excluded by PLIP EDO.73: 4 residues within 4Å: Chain I: P.143, G.189, P.191, R.478 Ligand excluded by PLIP EDO.74: 4 residues within 4Å: Chain C: R.62 Chain I: P.177, W.178, E.181 Ligand excluded by PLIP

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

NI.7: 8 residues within 4Å: Chain C: H.137, K.220, H.222, H.249, H.275, G.280 Ligands: NI.8, OH.11 4 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: C:H.249, C:H.275, OH.11, H2O.17 NI.8: 6 residues within 4Å: Chain C: H.137, H.139, K.220, D.363 Ligands: NI.7, OH.11 5 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: C:H.137, C:H.139, C:D.363, OH.11, H2O.16 NI.32: 8 residues within 4Å: Chain F: H.137, K.220, H.222, H.249, H.275, G.280 Ligands: NI.33, OH.36 4 PLIP interactions: 2 interactions with chain F, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: F:H.249, F:H.275, OH.36, H2O.43 NI.33: 6 residues within 4Å: Chain F: H.137, H.139, K.220, D.363 Ligands: NI.32, OH.36 5 PLIP interactions: 3 interactions with chain F, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: F:H.137, F:H.139, F:D.363, OH.36, H2O.42 NI.57: 8 residues within 4Å: Chain I: H.137, K.220, H.222, H.249, H.275, G.280 Ligands: NI.58, OH.61 4 PLIP interactions: 2 interactions with chain I, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: I:H.249, I:H.275, OH.61, H2O.69 NI.58: 6 residues within 4Å: Chain I: H.137, H.139, K.220, D.363 Ligands: NI.57, OH.61 5 PLIP interactions: 3 interactions with chain I, 1 Ligand-Ligand interactions, 1 Ligand-Water interactions Metal complexes: I:H.137, I:H.139, I:D.363, OH.61, H2O.68

3 x CAQ: CATECHOL(Covalent)

CAQ.9: 5 residues within 4Å: Chain C: K.169, C.322 Chain F: I.468, P.469, T.470 5 PLIP interactions: 3 interactions with chain F, 2 interactions with chain C Hydrophobic interactions: F:I.468, F:I.468, F:T.470 Hydrogen bonds: C:K.169 Water bridges: C:A.366 CAQ.34: 5 residues within 4Å: Chain F: K.169, C.322 Chain I: I.468, P.469, T.470 5 PLIP interactions: 2 interactions with chain F, 3 interactions with chain I Hydrogen bonds: F:K.169 Water bridges: F:A.366 Hydrophobic interactions: I:I.468, I:I.468, I:T.470 CAQ.59: 5 residues within 4Å: Chain C: I.468, P.469, T.470 Chain I: K.169, C.322 5 PLIP interactions: 2 interactions with chain I, 3 interactions with chain C Hydrogen bonds: I:K.169 Water bridges: I:A.366 Hydrophobic interactions: C:I.468, C:I.468, C:T.470

3 x OH: HYDROXIDE ION(Non-covalent)

OH.11: 8 residues within 4Å: Chain C: H.137, H.139, K.220, H.249, H.275, D.363 Ligands: NI.7, NI.8 No protein-ligand interaction detected (PLIP) OH.36: 8 residues within 4Å: Chain F: H.137, H.139, K.220, H.249, H.275, D.363 Ligands: NI.32, NI.33 No protein-ligand interaction detected (PLIP) OH.61: 8 residues within 4Å: Chain I: H.137, H.139, K.220, H.249, H.275, D.363 Ligands: NI.57, NI.58 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mazzei, L. et al., Inactivation of Urease by Catechol: Kinetics and Structure. J.Inorg.Biochem. (2016)

Release Date

2016-12-07

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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