SMTL ID : 6rkg.1

1.32 A RESOLUTION OF SPOROSARCINA PASTEURII UREASE INHIBITED IN THE PRESENCE OF NBPTO AT pH 7.5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.32 Å

Oligo State

hetero-3-3-3-mer

Ligands

54 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, K.10, T.85 Chain F: F.568, F.570 Ligand excluded by PLIP EDO.3: 5 residues within 4Å: Chain A: K.24, G.27, L.28, D.67, D.68 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain A: Y.32, I.77, D.79 Chain G: M.1 Ligand excluded by PLIP EDO.5: 3 residues within 4Å: Chain A: F.42, E.59, H.62 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.10: 4 residues within 4Å: Chain C: V.16, D.34, T.36, Y.38 Ligand excluded by PLIP EDO.11: 7 residues within 4Å: Chain B: P.66, T.69 Chain C: I.3, Q.7, S.11, Y.12 Chain F: I.329 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 H: R.34 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain C: Y.93, E.423, I.492, R.513, I.514 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain C: K.33, Y.35 Ligands: EDO.20 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain C: D.536, D.538, K.547, V.548, D.549, G.550 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain C: D.337, S.338, Y.544 Chain H: P.35, R.72, E.74 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain C: Y.35, Y.83, I.97, E.429 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain C: P.143, G.189, P.191, R.478 Chain I: V.483 Ligand excluded by PLIP EDO.19: 2 residues within 4Å: Chain C: V.309, P.557 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain C: K.33, D.34, Y.35 Ligands: EDO.14 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain C: D.317, M.320, V.321, Q.327 Chain G: D.79, Q.81, H.96 Ligand excluded by PLIP EDO.28: 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.29: 6 residues within 4Å: Chain D: N.4, A.6, K.10, T.85 Chain I: F.568, F.570 Ligand excluded by PLIP EDO.30: 5 residues within 4Å: Chain D: K.24, G.27, L.28, D.67, D.68 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain A: M.1 Chain D: Y.32, I.77, D.79 Ligand excluded by PLIP EDO.32: 3 residues within 4Å: Chain D: F.42, E.59, H.62 Ligand excluded by PLIP EDO.33: 3 residues within 4Å: Chain E: D.97 Chain I: P.229, D.233 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain F: V.16, D.34, T.36, Y.38 Ligand excluded by PLIP EDO.38: 7 residues within 4Å: Chain E: P.66, T.69 Chain F: I.3, Q.7, S.11, Y.12 Chain I: I.329 Ligand excluded by PLIP EDO.39: 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.40: 5 residues within 4Å: Chain F: Y.93, E.423, I.492, R.513, I.514 Ligand excluded by PLIP EDO.41: 3 residues within 4Å: Chain F: K.33, Y.35 Ligands: EDO.47 Ligand excluded by PLIP EDO.42: 6 residues within 4Å: Chain F: D.536, D.538, K.547, V.548, D.549, G.550 Ligand excluded by PLIP EDO.43: 6 residues within 4Å: Chain B: P.35, R.72, E.74 Chain F: D.337, S.338, Y.544 Ligand excluded by PLIP EDO.44: 4 residues within 4Å: Chain F: Y.35, Y.83, I.97, E.429 Ligand excluded by PLIP EDO.45: 5 residues within 4Å: Chain C: V.483 Chain F: P.143, G.189, P.191, R.478 Ligand excluded by PLIP EDO.46: 2 residues within 4Å: Chain F: V.309, P.557 Ligand excluded by PLIP EDO.47: 4 residues within 4Å: Chain F: K.33, D.34, Y.35 Ligands: EDO.41 Ligand excluded by PLIP EDO.48: 7 residues within 4Å: Chain A: D.79, Q.81, H.96 Chain F: D.317, M.320, V.321, Q.327 Ligand excluded by PLIP EDO.55: 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.56: 6 residues within 4Å: Chain C: F.568, F.570 Chain G: N.4, A.6, K.10, T.85 Ligand excluded by PLIP EDO.57: 5 residues within 4Å: Chain G: K.24, G.27, L.28, D.67, D.68 Ligand excluded by PLIP EDO.58: 4 residues within 4Å: Chain D: M.1 Chain G: Y.32, I.77, D.79 Ligand excluded by PLIP EDO.59: 3 residues within 4Å: Chain G: F.42, E.59, H.62 Ligand excluded by PLIP EDO.60: 3 residues within 4Å: Chain C: P.229, D.233 Chain H: D.97 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 C: I.329 Chain H: P.66, T.69 Chain I: I.3, Q.7, S.11, Y.12 Ligand excluded by PLIP EDO.66: 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.67: 5 residues within 4Å: Chain I: Y.93, E.423, I.492, R.513, I.514 Ligand excluded by PLIP EDO.68: 3 residues within 4Å: Chain I: K.33, Y.35 Ligands: EDO.74 Ligand excluded by PLIP EDO.69: 6 residues within 4Å: Chain I: D.536, D.538, K.547, V.548, D.549, G.550 Ligand excluded by PLIP EDO.70: 6 residues within 4Å: Chain E: P.35, R.72, E.74 Chain I: D.337, S.338, Y.544 Ligand excluded by PLIP EDO.71: 4 residues within 4Å: Chain I: Y.35, Y.83, I.97, E.429 Ligand excluded by PLIP EDO.72: 5 residues within 4Å: Chain F: V.483 Chain I: P.143, G.189, P.191, R.478 Ligand excluded by PLIP EDO.73: 2 residues within 4Å: Chain I: V.309, P.557 Ligand excluded by PLIP EDO.74: 4 residues within 4Å: Chain I: K.33, D.34, Y.35 Ligands: EDO.68 Ligand excluded by PLIP EDO.75: 7 residues within 4Å: Chain D: D.79, Q.81, H.96 Chain I: D.317, M.320, V.321, Q.327 Ligand excluded by PLIP

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

SO4.7: 2 residues within 4Å: Chain B: L.108, R.112 Ligand excluded by PLIP SO4.22: 2 residues within 4Å: Chain C: S.204, I.205 Ligand excluded by PLIP SO4.23: 3 residues within 4Å: Chain C: V.558, K.559, E.560 Ligand excluded by PLIP SO4.25: 9 residues within 4Å: Chain B: S.67, G.68, T.69 Chain C: S.11, Y.12, N.43, K.48 Chain F: K.326, I.329 Ligand excluded by PLIP SO4.26: 5 residues within 4Å: Chain C: K.511 Chain F: K.511 Chain I: K.511 Ligands: SO4.53, SO4.80 Ligand excluded by PLIP SO4.27: 1 residues within 4Å: Chain C: K.518 Ligand excluded by PLIP SO4.34: 2 residues within 4Å: Chain E: L.108, R.112 Ligand excluded by PLIP SO4.49: 2 residues within 4Å: Chain F: S.204, I.205 Ligand excluded by PLIP SO4.50: 3 residues within 4Å: Chain F: V.558, K.559, E.560 Ligand excluded by PLIP SO4.52: 9 residues within 4Å: Chain E: S.67, G.68, T.69 Chain F: S.11, Y.12, N.43, K.48 Chain I: K.326, I.329 Ligand excluded by PLIP SO4.53: 5 residues within 4Å: Chain C: K.511 Chain F: K.511 Chain I: K.511 Ligands: SO4.26, SO4.80 Ligand excluded by PLIP SO4.54: 1 residues within 4Å: Chain F: K.518 Ligand excluded by PLIP SO4.61: 2 residues within 4Å: Chain H: L.108, R.112 Ligand excluded by PLIP SO4.76: 2 residues within 4Å: Chain I: S.204, I.205 Ligand excluded by PLIP SO4.77: 3 residues within 4Å: Chain I: V.558, K.559, E.560 Ligand excluded by PLIP SO4.79: 9 residues within 4Å: Chain C: K.326, I.329 Chain H: S.67, G.68, T.69 Chain I: S.11, Y.12, N.43, K.48 Ligand excluded by PLIP SO4.80: 5 residues within 4Å: Chain C: K.511 Chain F: K.511 Chain I: K.511 Ligands: SO4.26, SO4.53 Ligand excluded by PLIP SO4.81: 1 residues within 4Å: Chain I: K.518 Ligand excluded by PLIP

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

NI.8: 7 residues within 4Å: Chain C: K.220, H.222, H.249, H.275, G.280 Ligands: NI.9, 2PA.24 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.249, C:H.275, C:G.280 NI.9: 6 residues within 4Å: Chain C: H.137, H.139, K.220, D.363 Ligands: NI.8, 2PA.24 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.137, C:H.139, C:D.363 NI.35: 7 residues within 4Å: Chain F: K.220, H.222, H.249, H.275, G.280 Ligands: NI.36, 2PA.51 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.249, F:H.275, F:G.280 NI.36: 6 residues within 4Å: Chain F: H.137, H.139, K.220, D.363 Ligands: NI.35, 2PA.51 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.137, F:H.139, F:D.363 NI.62: 7 residues within 4Å: Chain I: K.220, H.222, H.249, H.275, G.280 Ligands: NI.63, 2PA.78 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:H.249, I:H.275, I:G.280 NI.63: 6 residues within 4Å: Chain I: H.137, H.139, K.220, D.363 Ligands: NI.62, 2PA.78 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.24: 15 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, D.363, A.366, M.367 Ligands: NI.8, NI.9 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:H.323, C:R.339, C:A.366 2PA.51: 15 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, D.363, A.366, M.367 Ligands: NI.35, NI.36 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:H.323, F:R.339, F:A.366 2PA.78: 15 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, D.363, A.366, M.367 Ligands: NI.62, NI.63 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., The Impact of pH on Catalytically Critical Protein Conformational Changes: The Case of the Urease, a Nickel Enzyme. Chemistry (2019)

Release Date

2020-03-11

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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