SMTL ID : 6h8j.1

1.45 A resolution of Sporosarcina pasteurii urease inhibited in the presence of NBPTO

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

hetero-3-3-3-mer

Ligands

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

EDO.1: 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.2: 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.3: 7 residues within 4Å: Chain A: Y.32, V.36, M.76, I.77, D.79 Chain C: Q.472 Chain G: M.1 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: G.50, K.51, T.52, M.55 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain B: D.97 Chain F: P.229, D.233 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain C: D.34, T.36, Y.38 Ligand excluded by PLIP EDO.12: 2 residues within 4Å: Chain C: Y.35 Ligands: EDO.17 Ligand excluded by PLIP EDO.13: 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.14: 4 residues within 4Å: Chain C: Y.93, E.423, R.513, I.514 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain C: S.338, Y.544 Chain H: P.35, R.72, E.74 Ligand excluded by PLIP EDO.16: 7 residues within 4Å: Chain C: L.325, E.331, D.332, V.333, F.335 Chain H: Q.37 Chain I: G.46 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain C: Y.35, Y.83, I.97, E.429 Ligands: EDO.12 Ligand excluded by PLIP EDO.18: 8 residues within 4Å: Chain C: F.307, P.342, E.343, A.346, T.554, C.555, E.556, P.557 Ligand excluded by PLIP EDO.22: 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.23: 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.24: 7 residues within 4Å: Chain A: M.1 Chain D: Y.32, V.36, M.76, I.77, D.79 Chain F: Q.472 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain D: G.50, K.51, T.52, M.55 Ligand excluded by PLIP EDO.27: 3 residues within 4Å: Chain E: D.97 Chain I: P.229, D.233 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain F: D.34, T.36, Y.38 Ligand excluded by PLIP EDO.33: 2 residues within 4Å: Chain F: Y.35 Ligands: EDO.38 Ligand excluded by PLIP EDO.34: 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.35: 4 residues within 4Å: Chain F: Y.93, E.423, R.513, I.514 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain B: P.35, R.72, E.74 Chain F: S.338, Y.544 Ligand excluded by PLIP EDO.37: 7 residues within 4Å: Chain B: Q.37 Chain C: G.46 Chain F: L.325, E.331, D.332, V.333, F.335 Ligand excluded by PLIP EDO.38: 5 residues within 4Å: Chain F: Y.35, Y.83, I.97, E.429 Ligands: EDO.33 Ligand excluded by PLIP EDO.39: 8 residues within 4Å: Chain F: F.307, P.342, E.343, A.346, T.554, C.555, E.556, P.557 Ligand excluded by PLIP EDO.43: 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.44: 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.45: 7 residues within 4Å: Chain D: M.1 Chain G: Y.32, V.36, M.76, I.77, D.79 Chain I: Q.472 Ligand excluded by PLIP EDO.46: 4 residues within 4Å: Chain G: G.50, K.51, T.52, M.55 Ligand excluded by PLIP EDO.48: 3 residues within 4Å: Chain C: P.229, D.233 Chain H: D.97 Ligand excluded by PLIP EDO.53: 3 residues within 4Å: Chain I: D.34, T.36, Y.38 Ligand excluded by PLIP EDO.54: 2 residues within 4Å: Chain I: Y.35 Ligands: EDO.59 Ligand excluded by PLIP EDO.55: 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.56: 4 residues within 4Å: Chain I: Y.93, E.423, R.513, I.514 Ligand excluded by PLIP EDO.57: 5 residues within 4Å: Chain E: P.35, R.72, E.74 Chain I: S.338, Y.544 Ligand excluded by PLIP EDO.58: 7 residues within 4Å: Chain E: Q.37 Chain F: G.46 Chain I: L.325, E.331, D.332, V.333, F.335 Ligand excluded by PLIP EDO.59: 5 residues within 4Å: Chain I: Y.35, Y.83, I.97, E.429 Ligands: EDO.54 Ligand excluded by PLIP EDO.60: 8 residues within 4Å: Chain I: F.307, P.342, E.343, A.346, T.554, C.555, E.556, P.557 Ligand excluded by PLIP

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

SO4.5: 3 residues within 4Å: Chain A: M.70, E.71 Chain C: R.566 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Salt bridges: C:R.566 Hydrogen bonds: A:E.71 SO4.7: 2 residues within 4Å: Chain B: L.108, R.112 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.112 SO4.8: 8 residues within 4Å: Chain B: S.67, G.68, T.69 Chain C: S.11, N.43, K.48 Chain F: K.326, I.329 6 PLIP interactions: 1 interactions with chain F, 4 interactions with chain C, 1 interactions with chain B Water bridges: F:K.326, C:N.43, C:N.43 Hydrogen bonds: C:S.11, B:G.68 Salt bridges: C:K.48 SO4.19: 3 residues within 4Å: Chain C: V.558, K.559, E.560 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.559, C:E.560 Water bridges: C:P.557 Salt bridges: C:K.559 SO4.20: 1 residues within 4Å: Chain C: N.65 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.65 Water bridges: C:N.65 SO4.26: 3 residues within 4Å: Chain D: M.70, E.71 Chain F: R.566 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain F Hydrogen bonds: D:E.71 Salt bridges: F:R.566 SO4.28: 2 residues within 4Å: Chain E: L.108, R.112 1 PLIP interactions: 1 interactions with chain E Salt bridges: E:R.112 SO4.29: 8 residues within 4Å: Chain E: S.67, G.68, T.69 Chain F: S.11, N.43, K.48 Chain I: K.326, I.329 6 PLIP interactions: 4 interactions with chain F, 1 interactions with chain I, 1 interactions with chain E Hydrogen bonds: F:S.11, E:G.68 Water bridges: F:N.43, F:N.43, I:K.326 Salt bridges: F:K.48 SO4.40: 3 residues within 4Å: Chain F: V.558, K.559, E.560 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:K.559, F:E.560 Water bridges: F:P.557 Salt bridges: F:K.559 SO4.41: 1 residues within 4Å: Chain F: N.65 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:N.65 Water bridges: F:N.65 SO4.47: 3 residues within 4Å: Chain G: M.70, E.71 Chain I: R.566 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain G Salt bridges: I:R.566 Hydrogen bonds: G:E.71 SO4.49: 2 residues within 4Å: Chain H: L.108, R.112 1 PLIP interactions: 1 interactions with chain H Salt bridges: H:R.112 SO4.50: 8 residues within 4Å: Chain C: K.326, I.329 Chain H: S.67, G.68, T.69 Chain I: S.11, N.43, K.48 6 PLIP interactions: 1 interactions with chain C, 4 interactions with chain I, 1 interactions with chain H Water bridges: C:K.326, I:N.43, I:N.43 Hydrogen bonds: I:S.11, H:G.68 Salt bridges: I:K.48 SO4.61: 3 residues within 4Å: Chain I: V.558, K.559, E.560 4 PLIP interactions: 4 interactions with chain I Hydrogen bonds: I:K.559, I:E.560 Water bridges: I:P.557 Salt bridges: I:K.559 SO4.62: 1 residues within 4Å: Chain I: N.65 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:N.65 Water bridges: I:N.65

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

NI.9: 7 residues within 4Å: Chain C: K.220, H.222, H.249, H.275, G.280 Ligands: NI.10, 2PA.21 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.249, C:H.275 NI.10: 7 residues within 4Å: Chain C: H.137, H.139, K.220, D.363, A.366 Ligands: NI.9, 2PA.21 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.137, C:H.139, C:D.363 NI.30: 7 residues within 4Å: Chain F: K.220, H.222, H.249, H.275, G.280 Ligands: NI.31, 2PA.42 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:H.249, F:H.275 NI.31: 7 residues within 4Å: Chain F: H.137, H.139, K.220, D.363, A.366 Ligands: NI.30, 2PA.42 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.137, F:H.139, F:D.363 NI.51: 7 residues within 4Å: Chain I: K.220, H.222, H.249, H.275, G.280 Ligands: NI.52, 2PA.63 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:H.249, I:H.275 NI.52: 7 residues within 4Å: Chain I: H.137, H.139, K.220, D.363, A.366 Ligands: NI.51, 2PA.63 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:H.137, I:H.139, I:D.363

3 x 2PA: DIAMIDOPHOSPHATE(Non-covalent)

2PA.21: 16 residues within 4Å: Chain C: H.137, H.139, A.170, K.220, H.222, H.249, H.275, G.280, C.322, H.323, R.339, D.363, A.366, M.367 Ligands: NI.9, NI.10 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.323, C:R.339, C:A.366 2PA.42: 16 residues within 4Å: Chain F: H.137, H.139, A.170, K.220, H.222, H.249, H.275, G.280, C.322, H.323, R.339, D.363, A.366, M.367 Ligands: NI.30, NI.31 5 PLIP interactions: 5 interactions with chain F Hydrogen bonds: F:H.139, F:H.249, F:H.323, F:R.339, F:D.363 2PA.63: 16 residues within 4Å: Chain I: H.137, H.139, A.170, K.220, H.222, H.249, H.275, G.280, C.322, H.323, R.339, D.363, A.366, M.367 Ligands: NI.51, NI.52 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:H.323, I:R.339, I:A.366

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mazzei, L. et al., Insights into Urease Inhibition by N-( n-Butyl) Phosphoric Triamide through an Integrated Structural and Kinetic Approach. J.Agric.Food Chem. (2019)

Release Date

2019-06-12

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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