SMTL ID : 4goa.1

Crystal structure of jack bean urease inhibited with fluoride

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-hexamer

Ligands

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

NI.1: 7 residues within 4Å: Chain A: H.407, H.409, K.490, D.633 Ligands: NI.2, F.3, F.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.407, A:H.409, A:D.633, H2O.1 NI.2: 8 residues within 4Å: Chain A: K.490, H.492, H.519, H.545, G.550 Ligands: NI.1, F.3, F.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.519, A:H.545, H2O.1 NI.5: 7 residues within 4Å: Chain B: H.407, H.409, K.490, D.633 Ligands: NI.6, F.7, F.8 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.407, B:H.409, B:D.633, H2O.27 NI.6: 8 residues within 4Å: Chain B: K.490, H.492, H.519, H.545, G.550 Ligands: NI.5, F.7, F.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.519, B:H.545, H2O.27 NI.9: 7 residues within 4Å: Chain C: H.407, H.409, K.490, D.633 Ligands: NI.10, F.11, F.12 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.407, C:H.409, C:D.633, H2O.53 NI.10: 8 residues within 4Å: Chain C: K.490, H.492, H.519, H.545, G.550 Ligands: NI.9, F.11, F.12 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.519, C:H.545, H2O.53 NI.13: 7 residues within 4Å: Chain D: H.407, H.409, K.490, D.633 Ligands: NI.14, F.15, F.16 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.407, D:H.409, D:D.633, H2O.80 NI.14: 8 residues within 4Å: Chain D: K.490, H.492, H.519, H.545, G.550 Ligands: NI.13, F.15, F.16 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.519, D:H.545, H2O.80 NI.17: 7 residues within 4Å: Chain E: H.407, H.409, K.490, D.633 Ligands: NI.18, F.19, F.20 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.407, E:H.409, E:D.633, H2O.106 NI.18: 8 residues within 4Å: Chain E: K.490, H.492, H.519, H.545, G.550 Ligands: NI.17, F.19, F.20 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:H.519, E:H.545, H2O.106 NI.21: 7 residues within 4Å: Chain F: H.407, H.409, K.490, D.633 Ligands: NI.22, F.23, F.24 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.407, F:H.409, F:D.633, H2O.132 NI.22: 8 residues within 4Å: Chain F: K.490, H.492, H.519, H.545, G.550 Ligands: NI.21, F.23, F.24 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:H.519, F:H.545, H2O.133

12 x F: FLUORIDE ION(Non-covalent)

F.3: 7 residues within 4Å: Chain A: G.550, D.633, A.636, M.637 Ligands: NI.1, NI.2, F.4 No protein-ligand interaction detected (PLIP) F.4: 8 residues within 4Å: Chain A: H.407, K.490, H.545, G.550, D.633 Ligands: NI.1, NI.2, F.3 No protein-ligand interaction detected (PLIP) F.7: 7 residues within 4Å: Chain B: G.550, D.633, A.636, M.637 Ligands: NI.5, NI.6, F.8 No protein-ligand interaction detected (PLIP) F.8: 8 residues within 4Å: Chain B: H.407, K.490, H.545, G.550, D.633 Ligands: NI.5, NI.6, F.7 No protein-ligand interaction detected (PLIP) F.11: 7 residues within 4Å: Chain C: G.550, D.633, A.636, M.637 Ligands: NI.9, NI.10, F.12 No protein-ligand interaction detected (PLIP) F.12: 8 residues within 4Å: Chain C: H.407, K.490, H.545, G.550, D.633 Ligands: NI.9, NI.10, F.11 No protein-ligand interaction detected (PLIP) F.15: 7 residues within 4Å: Chain D: G.550, D.633, A.636, M.637 Ligands: NI.13, NI.14, F.16 No protein-ligand interaction detected (PLIP) F.16: 8 residues within 4Å: Chain D: H.407, K.490, H.545, G.550, D.633 Ligands: NI.13, NI.14, F.15 No protein-ligand interaction detected (PLIP) F.19: 7 residues within 4Å: Chain E: G.550, D.633, A.636, M.637 Ligands: NI.17, NI.18, F.20 No protein-ligand interaction detected (PLIP) F.20: 8 residues within 4Å: Chain E: H.407, K.490, H.545, G.550, D.633 Ligands: NI.17, NI.18, F.19 No protein-ligand interaction detected (PLIP) F.23: 7 residues within 4Å: Chain F: G.550, D.633, A.636, M.637 Ligands: NI.21, NI.22, F.24 No protein-ligand interaction detected (PLIP) F.24: 8 residues within 4Å: Chain F: H.407, K.490, H.545, G.550, D.633 Ligands: NI.21, NI.22, F.23 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Balasubramanian, A. et al., Crystal structure of jack bean urease inhibited with fluoride. To be Published

Release Date

2013-08-21

Peptides

Urease: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Urease

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