SMTL ID : 6qdy.1

The crystal structure of Sporosarcina pasteurii urease in complex with its substrate urea

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.42 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 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: 5 residues within 4Å: Chain A: Y.32, I.77, D.79 Chain C: Q.472 Chain G: M.1 Ligand excluded by PLIP EDO.4: 4 residues within 4Å: Chain B: D.97 Chain F: P.229, D.233, A.265 Ligand excluded by PLIP EDO.5: 2 residues within 4Å: Chain B: M.79, E.80 Ligand excluded by PLIP EDO.9: 4 residues within 4Å: Chain C: V.16, D.34, T.36, Y.38 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain C: Y.35, Y.83, I.97, E.429 Ligand excluded by PLIP EDO.11: 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.12: 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.13: 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.14: 3 residues within 4Å: Chain C: V.558, K.559, E.560 Ligand excluded by PLIP EDO.18: 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.19: 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.20: 5 residues within 4Å: Chain A: M.1 Chain D: Y.32, I.77, D.79 Chain F: Q.472 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain E: D.97 Chain I: P.229, D.233, A.265 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain E: M.79, E.80 Ligand excluded by PLIP EDO.26: 4 residues within 4Å: Chain F: V.16, D.34, T.36, Y.38 Ligand excluded by PLIP EDO.27: 4 residues within 4Å: Chain F: Y.35, Y.83, I.97, E.429 Ligand excluded by PLIP EDO.28: 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.29: 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.30: 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.31: 3 residues within 4Å: Chain F: V.558, K.559, E.560 Ligand excluded by PLIP EDO.35: 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.36: 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.37: 5 residues within 4Å: Chain D: M.1 Chain G: Y.32, I.77, D.79 Chain I: Q.472 Ligand excluded by PLIP EDO.38: 4 residues within 4Å: Chain C: P.229, D.233, A.265 Chain H: D.97 Ligand excluded by PLIP EDO.39: 2 residues within 4Å: Chain H: M.79, E.80 Ligand excluded by PLIP EDO.43: 4 residues within 4Å: Chain I: V.16, D.34, T.36, Y.38 Ligand excluded by PLIP EDO.44: 4 residues within 4Å: Chain I: Y.35, Y.83, I.97, E.429 Ligand excluded by PLIP EDO.45: 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.46: 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.47: 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.48: 3 residues within 4Å: Chain I: V.558, K.559, E.560 Ligand excluded by PLIP

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

SO4.6: 1 residues within 4Å: Chain B: R.112 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.112, B:R.112 Salt bridges: B:R.112 SO4.15: 8 residues within 4Å: Chain C: K.326, I.329 Chain H: S.67, G.68 Chain I: S.11, Y.12, N.43, K.48 7 PLIP interactions: 2 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 Salt bridges: C:K.326, I:K.48 Hydrogen bonds: I:S.11, H:G.68 SO4.23: 1 residues within 4Å: Chain E: R.112 3 PLIP interactions: 3 interactions with chain E Water bridges: E:R.112, E:R.112 Salt bridges: E:R.112 SO4.32: 8 residues within 4Å: Chain B: S.67, G.68 Chain C: S.11, Y.12, N.43, K.48 Chain F: K.326, I.329 7 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B, 2 interactions with chain F Hydrogen bonds: C:S.11, B:G.68 Water bridges: C:N.43, C:N.43, F:K.326 Salt bridges: C:K.48, F:K.326 SO4.40: 1 residues within 4Å: Chain H: R.112 3 PLIP interactions: 3 interactions with chain H Water bridges: H:R.112, H:R.112 Salt bridges: H:R.112 SO4.49: 8 residues within 4Å: Chain E: S.67, G.68 Chain F: S.11, Y.12, N.43, K.48 Chain I: K.326, I.329 7 PLIP interactions: 4 interactions with chain F, 2 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, I:K.326

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.16, URE.17 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:H.249, C:H.275, URE.17 NI.8: 7 residues within 4Å: Chain C: H.137, H.139, K.220, D.363 Ligands: NI.7, F.16, URE.17 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.137, C:H.139, C:D.363 NI.24: 8 residues within 4Å: Chain F: K.220, H.222, H.249, H.275, G.280 Ligands: NI.25, F.33, URE.34 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Ligand interactions Metal complexes: F:H.249, F:H.275, URE.34 NI.25: 7 residues within 4Å: Chain F: H.137, H.139, K.220, D.363 Ligands: NI.24, F.33, URE.34 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.137, F:H.139, F:D.363 NI.41: 8 residues within 4Å: Chain I: K.220, H.222, H.249, H.275, G.280 Ligands: NI.42, F.50, URE.51 2 PLIP interactions: 2 interactions with chain I Metal complexes: I:H.249, I:H.275 NI.42: 7 residues within 4Å: Chain I: H.137, H.139, K.220, D.363 Ligands: NI.41, F.50, URE.51 3 PLIP interactions: 3 interactions with chain I Metal complexes: I:H.137, I:H.139, I:D.363

3 x F: FLUORIDE ION(Non-covalent)

F.16: 8 residues within 4Å: Chain C: H.137, K.220, H.275, G.280, D.363 Ligands: NI.7, NI.8, URE.17 No protein-ligand interaction detected (PLIP) F.33: 8 residues within 4Å: Chain F: H.137, K.220, H.275, G.280, D.363 Ligands: NI.24, NI.25, URE.34 No protein-ligand interaction detected (PLIP) F.50: 8 residues within 4Å: Chain I: H.137, K.220, H.275, G.280, D.363 Ligands: NI.41, NI.42, URE.51 No protein-ligand interaction detected (PLIP)

3 x URE: UREA(Non-functional Binders)

URE.17: 15 residues within 4Å: Chain C: 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.7, NI.8, F.16 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:A.366 URE.34: 15 residues within 4Å: Chain F: 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.24, NI.25, F.33 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:A.366 URE.51: 15 residues within 4Å: Chain I: 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.41, NI.42, F.50 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:H.249, I:A.366, I:A.366

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mazzei, L. et al., The Structure of the Elusive Urease-Urea Complex Unveils the Mechanism of a Paradigmatic Nickel-Dependent Enzyme. Angew.Chem.Int.Ed.Engl. (2019)

Release Date

2019-11-13

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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