SMTL ID : 4cex.1

1.59 A resolution Fluoride inhibited Sporosarcina pasteurii urease

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.59 Å

Oligo State

hetero-3-3-3-mer

Ligands

33 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 I: V.309, N.310, K.559 Ligand excluded by PLIP 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: 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.4: 3 residues within 4Å: Chain B: D.101 Chain I: P.229, D.233 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain B: N.68, I.69, E.86 Chain C: M.1 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain C: D.34, T.36, Y.38 Ligand excluded by PLIP EDO.12: 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.13: 5 residues within 4Å: Chain C: L.253, L.325, D.332, F.335 Chain F: G.46 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain C: Y.93, E.423, I.492, R.513, I.514 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain C: Y.35, Y.83, I.97, E.429 Ligand excluded by PLIP EDO.16: 4 residues within 4Å: Chain C: P.177, W.178, E.181 Chain F: R.62 Ligand excluded by PLIP EDO.19: 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.20: 6 residues within 4Å: Chain D: K.24, G.27, L.28, K.29, D.67, D.68 Ligand excluded by PLIP EDO.21: 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.22: 3 residues within 4Å: Chain C: P.229, D.233 Chain E: D.101 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain E: N.68, I.69, E.86 Chain F: M.1 Ligand excluded by PLIP EDO.29: 3 residues within 4Å: Chain F: D.34, T.36, Y.38 Ligand excluded by PLIP EDO.30: 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.31: 5 residues within 4Å: Chain F: L.253, L.325, D.332, F.335 Chain I: G.46 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain F: Y.93, E.423, I.492, R.513, I.514 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain F: Y.35, Y.83, I.97, E.429 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain F: P.177, W.178, E.181 Chain I: R.62 Ligand excluded by PLIP EDO.37: 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.38: 6 residues within 4Å: Chain G: K.24, G.27, L.28, K.29, D.67, D.68 Ligand excluded by PLIP EDO.39: 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.40: 3 residues within 4Å: Chain F: P.229, D.233 Chain H: D.101 Ligand excluded by PLIP EDO.41: 4 residues within 4Å: Chain H: N.68, I.69, E.86 Chain I: M.1 Ligand excluded by PLIP EDO.47: 3 residues within 4Å: Chain I: D.34, T.36, Y.38 Ligand excluded by PLIP EDO.48: 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.49: 5 residues within 4Å: Chain C: G.46 Chain I: L.253, L.325, D.332, F.335 Ligand excluded by PLIP EDO.50: 5 residues within 4Å: Chain I: Y.93, E.423, I.492, R.513, I.514 Ligand excluded by PLIP EDO.51: 4 residues within 4Å: Chain I: Y.35, Y.83, I.97, E.429 Ligand excluded by PLIP EDO.52: 4 residues within 4Å: Chain C: R.62 Chain I: P.177, W.178, E.181 Ligand excluded by PLIP

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

SO4.6: 2 residues within 4Å: Chain B: L.112, R.116 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Q.115 Salt bridges: B:R.116 SO4.17: 3 residues within 4Å: Chain C: V.558, K.559, E.560 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.559, C:E.560 Water bridges: C:P.557 SO4.18: 5 residues within 4Å: Chain C: K.511 Chain F: K.511 Chain I: K.511 Ligands: SO4.36, SO4.54 7 PLIP interactions: 2 interactions with chain C, 2 interactions with chain I, 3 interactions with chain F Water bridges: C:K.511, I:K.511, F:K.511, F:K.511 Salt bridges: C:K.511, I:K.511, F:K.511 SO4.24: 2 residues within 4Å: Chain E: L.112, R.116 2 PLIP interactions: 2 interactions with chain E Water bridges: E:Q.115 Salt bridges: E:R.116 SO4.35: 3 residues within 4Å: Chain F: V.558, K.559, E.560 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:K.559, F:E.560 Water bridges: F:P.557 SO4.36: 5 residues within 4Å: Chain C: K.511 Chain F: K.511 Chain I: K.511 Ligands: SO4.18, SO4.54 7 PLIP interactions: 2 interactions with chain C, 3 interactions with chain I, 2 interactions with chain F Water bridges: C:K.511, I:K.511, I:K.511, F:K.511 Salt bridges: C:K.511, I:K.511, F:K.511 SO4.42: 2 residues within 4Å: Chain H: L.112, R.116 2 PLIP interactions: 2 interactions with chain H Water bridges: H:Q.115 Salt bridges: H:R.116 SO4.53: 3 residues within 4Å: Chain I: V.558, K.559, E.560 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:K.559, I:E.560 Water bridges: I:P.557 SO4.54: 5 residues within 4Å: Chain C: K.511 Chain F: K.511 Chain I: K.511 Ligands: SO4.18, SO4.36 7 PLIP interactions: 2 interactions with chain I, 3 interactions with chain C, 2 interactions with chain F Water bridges: I:K.511, C:K.511, C:K.511, F:K.511 Salt bridges: I:K.511, C:K.511, F:K.511

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

NI.7: 8 residues within 4Å: Chain C: K.220, H.222, H.249, H.275, G.280 Ligands: NI.8, F.9, F.10 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.249, C:H.275 NI.8: 7 residues within 4Å: Chain C: H.137, H.139, K.220, D.363 Ligands: NI.7, F.9, F.10 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.137, C:H.139, C:D.363, H2O.20 NI.25: 8 residues within 4Å: Chain F: K.220, H.222, H.249, H.275, G.280 Ligands: NI.26, F.27, F.28 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:H.249, F:H.275 NI.26: 7 residues within 4Å: Chain F: H.137, H.139, K.220, D.363 Ligands: NI.25, F.27, F.28 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.137, F:H.139, F:D.363, H2O.51 NI.43: 8 residues within 4Å: Chain I: K.220, H.222, H.249, H.275, G.280 Ligands: NI.44, F.45, F.46 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:H.249, I:H.275 NI.44: 7 residues within 4Å: Chain I: H.137, H.139, K.220, D.363 Ligands: NI.43, F.45, F.46 4 PLIP interactions: 3 interactions with chain I, 1 Ligand-Water interactions Metal complexes: I:H.137, I:H.139, I:D.363, H2O.83

6 x F: FLUORIDE ION(Non-covalent)

F.9: 7 residues within 4Å: Chain C: H.137, K.220, H.275, D.363 Ligands: NI.7, NI.8, F.10 No protein-ligand interaction detected (PLIP) F.10: 9 residues within 4Å: Chain C: A.170, K.220, H.222, H.249, H.275, G.280 Ligands: NI.7, NI.8, F.9 No protein-ligand interaction detected (PLIP) F.27: 7 residues within 4Å: Chain F: H.137, K.220, H.275, D.363 Ligands: NI.25, NI.26, F.28 No protein-ligand interaction detected (PLIP) F.28: 9 residues within 4Å: Chain F: A.170, K.220, H.222, H.249, H.275, G.280 Ligands: NI.25, NI.26, F.27 No protein-ligand interaction detected (PLIP) F.45: 7 residues within 4Å: Chain I: H.137, K.220, H.275, D.363 Ligands: NI.43, NI.44, F.46 No protein-ligand interaction detected (PLIP) F.46: 9 residues within 4Å: Chain I: A.170, K.220, H.222, H.249, H.275, G.280 Ligands: NI.43, NI.44, F.45 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Benini, S. et al., Fluoride Inhibition of Sporosarcina Pasteurii Urease: Structure and Thermodynamics. J.Biol.Inorg.Chem. (2014)

Release Date

2014-08-27

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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