SMTL ID : 4ac7.1

The crystal structure of Sporosarcina pasteurii urease in complex with citrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-3-3-3-mer

Ligands

30 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: 5 residues within 4Å: Chain A: N.4, A.6, 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.10: 3 residues within 4Å: Chain C: D.34, T.36, Y.38 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain C: D.286, A.289, I.537, D.538, I.539 Chain E: R.38 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain C: L.253, L.325, F.335 Chain E: Q.41 Chain F: G.46 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain C: Y.93, E.423, R.513, I.514 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain C: Y.35, Y.83, I.97, E.429 Ligand excluded by PLIP EDO.15: 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: 5 residues within 4Å: Chain C: F.568, F.570 Chain D: N.4, A.6, 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.28: 3 residues within 4Å: Chain F: D.34, T.36, Y.38 Ligand excluded by PLIP EDO.29: 6 residues within 4Å: Chain F: D.286, A.289, I.537, D.538, I.539 Chain H: R.38 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain F: L.253, L.325, F.335 Chain H: Q.41 Chain I: G.46 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain F: Y.93, E.423, R.513, I.514 Ligand excluded by PLIP EDO.32: 4 residues within 4Å: Chain F: Y.35, Y.83, I.97, E.429 Ligand excluded by PLIP EDO.33: 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: 5 residues within 4Å: Chain F: F.568, F.570 Chain G: N.4, A.6, 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.46: 3 residues within 4Å: Chain I: D.34, T.36, Y.38 Ligand excluded by PLIP EDO.47: 6 residues within 4Å: Chain B: R.38 Chain I: D.286, A.289, I.537, D.538, I.539 Ligand excluded by PLIP EDO.48: 5 residues within 4Å: Chain B: Q.41 Chain C: G.46 Chain I: L.253, L.325, F.335 Ligand excluded by PLIP EDO.49: 4 residues within 4Å: Chain I: Y.93, E.423, R.513, I.514 Ligand excluded by PLIP EDO.50: 4 residues within 4Å: Chain I: Y.35, Y.83, I.97, E.429 Ligand excluded by PLIP EDO.51: 4 residues within 4Å: Chain C: R.62 Chain I: P.177, W.178, E.181 Ligand excluded by PLIP

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

SO4.5: 1 residues within 4Å: Chain B: R.116 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Q.115 Salt bridges: B:R.116 SO4.16: 2 residues within 4Å: Chain C: S.204, I.205 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:I.205 Water bridges: C:S.203, C:A.206 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 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain I, 1 interactions with chain F Salt bridges: C:K.511, I:K.511, F:K.511 SO4.23: 1 residues within 4Å: Chain E: R.116 2 PLIP interactions: 2 interactions with chain E Water bridges: E:Q.115 Salt bridges: E:R.116 SO4.34: 2 residues within 4Å: Chain F: S.204, I.205 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:I.205 Water bridges: F:S.203, F:A.206 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 3 PLIP interactions: 1 interactions with chain I, 1 interactions with chain C, 1 interactions with chain F Salt bridges: I:K.511, C:K.511, F:K.511 SO4.41: 1 residues within 4Å: Chain H: R.116 2 PLIP interactions: 2 interactions with chain H Water bridges: H:Q.115 Salt bridges: H:R.116 SO4.52: 2 residues within 4Å: Chain I: S.204, I.205 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:I.205 Water bridges: I:S.203, I:A.206 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 3 PLIP interactions: 1 interactions with chain I, 1 interactions with chain C, 1 interactions with chain F Salt bridges: I:K.511, C:K.511, F:K.511

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

NI.6: 9 residues within 4Å: Chain C: H.137, K.220, H.222, H.249, H.275, G.280 Ligands: NI.7, OH.8, FLC.9 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:H.249, C:H.275, OH.8 NI.7: 7 residues within 4Å: Chain C: H.137, H.139, K.220, D.363 Ligands: NI.6, OH.8, FLC.9 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:H.137, C:H.139, C:D.363, OH.8 NI.24: 9 residues within 4Å: Chain F: H.137, K.220, H.222, H.249, H.275, G.280 Ligands: NI.25, OH.26, FLC.27 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: F:H.249, F:H.275, OH.26 NI.25: 7 residues within 4Å: Chain F: H.137, H.139, K.220, D.363 Ligands: NI.24, OH.26, FLC.27 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: F:H.137, F:H.139, F:D.363, OH.26 NI.42: 9 residues within 4Å: Chain I: H.137, K.220, H.222, H.249, H.275, G.280 Ligands: NI.43, OH.44, FLC.45 3 PLIP interactions: 2 interactions with chain I, 1 Ligand-Ligand interactions Metal complexes: I:H.249, I:H.275, OH.44 NI.43: 7 residues within 4Å: Chain I: H.137, H.139, K.220, D.363 Ligands: NI.42, OH.44, FLC.45 4 PLIP interactions: 3 interactions with chain I, 1 Ligand-Ligand interactions Metal complexes: I:H.137, I:H.139, I:D.363, OH.44

3 x OH: HYDROXIDE ION(Non-covalent)

OH.8: 7 residues within 4Å: Chain C: H.137, K.220, H.275, D.363 Ligands: NI.6, NI.7, FLC.9 No protein-ligand interaction detected (PLIP) OH.26: 7 residues within 4Å: Chain F: H.137, K.220, H.275, D.363 Ligands: NI.24, NI.25, FLC.27 No protein-ligand interaction detected (PLIP) OH.44: 7 residues within 4Å: Chain I: H.137, K.220, H.275, D.363 Ligands: NI.42, NI.43, FLC.45 No protein-ligand interaction detected (PLIP)

3 x FLC: CITRATE ANION(Non-covalent)

FLC.9: 16 residues within 4Å: Chain C: H.139, K.169, A.170, K.220, H.222, D.224, H.249, G.280, H.323, R.339, D.363, A.366, M.367 Ligands: NI.6, NI.7, OH.8 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:M.367 Hydrogen bonds: C:A.366 Water bridges: C:R.339, C:R.339, C:R.339, C:A.366 Salt bridges: C:H.137, C:H.139, C:H.222, C:H.249, C:H.249, C:H.275, C:H.323, C:R.339 FLC.27: 16 residues within 4Å: Chain F: H.139, K.169, A.170, K.220, H.222, D.224, H.249, G.280, H.323, R.339, D.363, A.366, M.367 Ligands: NI.24, NI.25, OH.26 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:M.367 Hydrogen bonds: F:A.366 Water bridges: F:R.339, F:R.339, F:R.339, F:A.366 Salt bridges: F:H.137, F:H.139, F:H.222, F:H.249, F:H.249, F:H.275, F:H.323, F:R.339 FLC.45: 16 residues within 4Å: Chain I: H.139, K.169, A.170, K.220, H.222, D.224, H.249, G.280, H.323, R.339, D.363, A.366, M.367 Ligands: NI.42, NI.43, OH.44 14 PLIP interactions: 14 interactions with chain I Hydrophobic interactions: I:M.367 Hydrogen bonds: I:A.366 Water bridges: I:R.339, I:R.339, I:R.339, I:A.366 Salt bridges: I:H.137, I:H.139, I:H.222, I:H.249, I:H.249, I:H.275, I:H.323, I:R.339

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Benini, S. et al., The Crystal Structure of Sporosarcina Pasteurii Urease in a Complex with Citrate Provides New Hints for Inhibitor Design. J.Biol.Inorg.Chem. (2013)

Release Date

2013-01-16

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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