SMTL ID : 7zcy.1

Sporosarcina pasteurii urease (SPU) co-crystallized in the presence of an Ebselen-derivative and bound to Se atoms

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

hetero-3-3-3-mer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: M.1 Chain D: Y.32, I.77, D.79 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: 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.5: 3 residues within 4Å: Chain F: V.558, K.559, E.560 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: F.42, E.59, H.62 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain C: A.170, D.224, H.323 Chain I: G.45, G.46 Ligands: SO4.15 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain C: V.16, D.34, T.36, T.37, Y.38 Ligand excluded by PLIP EDO.20: 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.21: 5 residues within 4Å: Chain B: S.67, G.68 Chain C: Y.12, N.43, K.48 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain B: G.88 Chain C: D.107, G.108 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain C: P.229, D.233, A.265 Chain H: D.97 Ligand excluded by PLIP EDO.24: 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.25: 4 residues within 4Å: Chain C: K.497, T.516, K.518 Ligands: SO4.18 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain C: I.350, R.388, E.551, V.552, L.553 Ligands: IU9.14 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain C: Y.35, Y.83, I.97, E.429 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain C: E.343, E.542, T.543, Y.544 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain C: Y.93, E.423, R.513, I.514 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain C: T.554, C.555, E.556 Ligands: IU9.14 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain B: R.9 Chain C: D.26, W.28 Ligand excluded by PLIP EDO.32: 1 residues within 4Å: Chain C: A.506 Ligand excluded by PLIP EDO.35: 4 residues within 4Å: Chain D: M.1 Chain G: Y.32, I.77, D.79 Ligand excluded by PLIP EDO.36: 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.37: 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.39: 3 residues within 4Å: Chain I: V.558, K.559, E.560 Ligand excluded by PLIP EDO.40: 3 residues within 4Å: Chain D: F.42, E.59, H.62 Ligand excluded by PLIP EDO.47: 6 residues within 4Å: Chain C: G.45, G.46 Chain F: A.170, D.224, H.323 Ligands: SO4.49 Ligand excluded by PLIP EDO.53: 5 residues within 4Å: Chain F: V.16, D.34, T.36, T.37, Y.38 Ligand excluded by PLIP EDO.54: 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.55: 5 residues within 4Å: Chain E: S.67, G.68 Chain F: Y.12, N.43, K.48 Ligand excluded by PLIP EDO.56: 3 residues within 4Å: Chain E: G.88 Chain F: D.107, G.108 Ligand excluded by PLIP EDO.57: 4 residues within 4Å: Chain B: D.97 Chain F: P.229, D.233, A.265 Ligand excluded by PLIP EDO.58: 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.59: 4 residues within 4Å: Chain F: K.497, T.516, K.518 Ligands: SO4.52 Ligand excluded by PLIP EDO.60: 6 residues within 4Å: Chain F: I.350, R.388, E.551, V.552, L.553 Ligands: IU9.48 Ligand excluded by PLIP EDO.61: 4 residues within 4Å: Chain F: Y.35, Y.83, I.97, E.429 Ligand excluded by PLIP EDO.62: 4 residues within 4Å: Chain F: E.343, E.542, T.543, Y.544 Ligand excluded by PLIP EDO.63: 4 residues within 4Å: Chain F: Y.93, E.423, R.513, I.514 Ligand excluded by PLIP EDO.64: 4 residues within 4Å: Chain F: T.554, C.555, E.556 Ligands: IU9.48 Ligand excluded by PLIP EDO.65: 3 residues within 4Å: Chain E: R.9 Chain F: D.26, W.28 Ligand excluded by PLIP EDO.66: 1 residues within 4Å: Chain F: A.506 Ligand excluded by PLIP EDO.69: 4 residues within 4Å: Chain A: Y.32, I.77, D.79 Chain G: M.1 Ligand excluded by PLIP EDO.70: 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.71: 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.73: 3 residues within 4Å: Chain C: V.558, K.559, E.560 Ligand excluded by PLIP EDO.74: 3 residues within 4Å: Chain G: F.42, E.59, H.62 Ligand excluded by PLIP EDO.81: 6 residues within 4Å: Chain F: G.45, G.46 Chain I: A.170, D.224, H.323 Ligands: SO4.83 Ligand excluded by PLIP EDO.87: 5 residues within 4Å: Chain I: V.16, D.34, T.36, T.37, Y.38 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: 5 residues within 4Å: Chain H: S.67, G.68 Chain I: Y.12, N.43, K.48 Ligand excluded by PLIP EDO.90: 3 residues within 4Å: Chain H: G.88 Chain I: D.107, G.108 Ligand excluded by PLIP EDO.91: 4 residues within 4Å: Chain E: D.97 Chain I: P.229, D.233, A.265 Ligand excluded by PLIP EDO.92: 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: 4 residues within 4Å: Chain I: K.497, T.516, K.518 Ligands: SO4.86 Ligand excluded by PLIP EDO.94: 6 residues within 4Å: Chain I: I.350, R.388, E.551, V.552, L.553 Ligands: IU9.82 Ligand excluded by PLIP EDO.95: 4 residues within 4Å: Chain I: Y.35, Y.83, I.97, E.429 Ligand excluded by PLIP EDO.96: 4 residues within 4Å: Chain I: E.343, E.542, T.543, Y.544 Ligand excluded by PLIP EDO.97: 4 residues within 4Å: Chain I: Y.93, E.423, R.513, I.514 Ligand excluded by PLIP EDO.98: 4 residues within 4Å: Chain I: T.554, C.555, E.556 Ligands: IU9.82 Ligand excluded by PLIP EDO.99: 3 residues within 4Å: Chain H: R.9 Chain I: D.26, W.28 Ligand excluded by PLIP EDO.100: 1 residues within 4Å: Chain I: A.506 Ligand excluded by PLIP

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

SO4.4: 3 residues within 4Å: Chain A: M.70, E.71 Chain C: R.566 Ligand excluded by PLIP SO4.7: 3 residues within 4Å: Chain B: T.25, I.26, R.27 Ligand excluded by PLIP SO4.8: 2 residues within 4Å: Chain B: L.108, R.112 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain B: L.52, K.119, G.120, V.121 Ligand excluded by PLIP SO4.15: 9 residues within 4Å: Chain C: A.170, H.222, E.223, D.224, H.249, G.280, H.323, R.339 Ligands: EDO.13 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain F: S.204, I.205 Ligand excluded by PLIP SO4.17: 5 residues within 4Å: Chain C: K.511 Chain F: K.511 Chain I: K.511 Ligands: SO4.51, SO4.85 Ligand excluded by PLIP SO4.18: 2 residues within 4Å: Chain C: K.518 Ligands: EDO.25 Ligand excluded by PLIP SO4.38: 3 residues within 4Å: Chain D: M.70, E.71 Chain F: R.566 Ligand excluded by PLIP SO4.41: 3 residues within 4Å: Chain E: T.25, I.26, R.27 Ligand excluded by PLIP SO4.42: 2 residues within 4Å: Chain E: L.108, R.112 Ligand excluded by PLIP SO4.43: 4 residues within 4Å: Chain E: L.52, K.119, G.120, V.121 Ligand excluded by PLIP SO4.49: 9 residues within 4Å: Chain F: A.170, H.222, E.223, D.224, H.249, G.280, H.323, R.339 Ligands: EDO.47 Ligand excluded by PLIP SO4.50: 2 residues within 4Å: Chain I: S.204, I.205 Ligand excluded by PLIP SO4.51: 5 residues within 4Å: Chain C: K.511 Chain F: K.511 Chain I: K.511 Ligands: SO4.17, SO4.85 Ligand excluded by PLIP SO4.52: 2 residues within 4Å: Chain F: K.518 Ligands: EDO.59 Ligand excluded by PLIP SO4.72: 3 residues within 4Å: Chain G: M.70, E.71 Chain I: R.566 Ligand excluded by PLIP SO4.75: 3 residues within 4Å: Chain H: T.25, I.26, R.27 Ligand excluded by PLIP SO4.76: 2 residues within 4Å: Chain H: L.108, R.112 Ligand excluded by PLIP SO4.77: 4 residues within 4Å: Chain H: L.52, K.119, G.120, V.121 Ligand excluded by PLIP SO4.83: 9 residues within 4Å: Chain I: A.170, H.222, E.223, D.224, H.249, G.280, H.323, R.339 Ligands: EDO.81 Ligand excluded by PLIP SO4.84: 2 residues within 4Å: Chain C: S.204, I.205 Ligand excluded by PLIP SO4.85: 5 residues within 4Å: Chain C: K.511 Chain F: K.511 Chain I: K.511 Ligands: SO4.17, SO4.51 Ligand excluded by PLIP SO4.86: 2 residues within 4Å: Chain I: K.518 Ligands: EDO.93 Ligand excluded by PLIP

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

NI.10: 7 residues within 4Å: Chain C: K.220, H.222, H.249, H.275, G.280 Ligands: NI.11, OH.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.11, OH.12 NI.11: 6 residues within 4Å: Chain C: H.137, H.139, K.220, D.363 Ligands: NI.10, OH.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.11, OH.12 NI.44: 7 residues within 4Å: Chain F: K.220, H.222, H.249, H.275, G.280 Ligands: NI.45, OH.46 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.41, OH.46 NI.45: 6 residues within 4Å: Chain F: H.137, H.139, K.220, D.363 Ligands: NI.44, OH.46 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.41, OH.46 NI.78: 7 residues within 4Å: Chain I: K.220, H.222, H.249, H.275, G.280 Ligands: NI.79, OH.80 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.70, OH.80 NI.79: 6 residues within 4Å: Chain I: H.137, H.139, K.220, D.363 Ligands: NI.78, OH.80 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.70, OH.80

3 x OH: HYDROXIDE ION(Non-covalent)

OH.12: 8 residues within 4Å: Chain C: H.137, K.220, H.249, H.275, G.280, D.363 Ligands: NI.10, NI.11 No protein-ligand interaction detected (PLIP) OH.46: 8 residues within 4Å: Chain F: H.137, K.220, H.249, H.275, G.280, D.363 Ligands: NI.44, NI.45 No protein-ligand interaction detected (PLIP) OH.80: 8 residues within 4Å: Chain I: H.137, K.220, H.249, H.275, G.280, D.363 Ligands: NI.78, NI.79 No protein-ligand interaction detected (PLIP)

3 x IU9: N-(2-chloranyl-4-fluoranyl-phenyl)-2-selanyl-benzamide(Non-covalent)

IU9.14: 8 residues within 4Å: Chain C: I.350, Q.387, R.388, T.554, C.555, E.556 Ligands: EDO.26, EDO.30 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:Q.387, C:Q.387, C:E.556 Hydrogen bonds: C:R.388 Water bridges: C:T.554 pi-Cation interactions: C:R.388 IU9.48: 8 residues within 4Å: Chain F: I.350, Q.387, R.388, T.554, C.555, E.556 Ligands: EDO.60, EDO.64 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:Q.387, F:Q.387, F:E.556 Hydrogen bonds: F:R.388 Water bridges: F:T.554 pi-Cation interactions: F:R.388 IU9.82: 8 residues within 4Å: Chain I: I.350, Q.387, R.388, T.554, C.555, E.556 Ligands: EDO.94, EDO.98 6 PLIP interactions: 6 interactions with chain I Hydrophobic interactions: I:Q.387, I:Q.387, I:E.556 Hydrogen bonds: I:R.388 Water bridges: I:T.554 pi-Cation interactions: I:R.388

6 x SE: SELENIUM ATOM(Non-covalent)

SE.33: 3 residues within 4Å: Chain C: C.322 Chain I: I.468 Ligands: SE.34 No protein-ligand interaction detected (PLIP) SE.34: 3 residues within 4Å: Chain C: C.322 Chain I: T.470 Ligands: SE.33 No protein-ligand interaction detected (PLIP) SE.67: 3 residues within 4Å: Chain C: I.468 Chain F: C.322 Ligands: SE.68 No protein-ligand interaction detected (PLIP) SE.68: 3 residues within 4Å: Chain C: T.470 Chain F: C.322 Ligands: SE.67 No protein-ligand interaction detected (PLIP) SE.101: 3 residues within 4Å: Chain F: I.468 Chain I: C.322 Ligands: SE.102 No protein-ligand interaction detected (PLIP) SE.102: 3 residues within 4Å: Chain F: T.470 Chain I: C.322 Ligands: SE.101 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Macegoniuk, K. et al., Optimized Ebselen-Based Inhibitors of Bacterial Ureases with Nontypical Mode of Action. J.Med.Chem. (2023)

Release Date

2023-04-19

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

Related Entries With Identical Sequence