SMTL ID : 4g7e.1

Crystal structure of pigeon pea urease

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-oligomer

Ligands

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

NI.1: 6 residues within 4Å: Chain A: K.490, H.492, H.519, H.545, G.550 Ligands: NI.2 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.519, A:H.545, H2O.1, H2O.3 NI.2: 5 residues within 4Å: Chain A: H.407, H.409, K.490, D.633 Ligands: NI.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.407, A:H.409, A:D.633, H2O.2, H2O.3 NI.3: 5 residues within 4Å: Chain B: H.407, H.409, K.490, D.633 Ligands: NI.4 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.407, B:H.409, B:D.633, H2O.300, H2O.301 NI.4: 7 residues within 4Å: Chain B: H.407, K.490, H.492, H.519, H.545, G.550 Ligands: NI.3 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:H.519, B:H.545, H2O.300, H2O.303 NI.6: 6 residues within 4Å: Chain C: K.490, H.492, H.519, H.545, G.550 Ligands: NI.7 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.519, C:H.545, H2O.657, H2O.659 NI.7: 5 residues within 4Å: Chain C: H.407, H.409, K.490, D.633 Ligands: NI.6 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:H.407, C:H.409, C:D.633, H2O.658, H2O.659 NI.8: 5 residues within 4Å: Chain D: H.407, H.409, K.490, D.633 Ligands: NI.9 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.407, D:H.409, D:D.633, H2O.956, H2O.957 NI.9: 7 residues within 4Å: Chain D: H.407, K.490, H.492, H.519, H.545, G.550 Ligands: NI.8 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:H.519, D:H.545, H2O.956, H2O.959 NI.11: 6 residues within 4Å: Chain E: K.490, H.492, H.519, H.545, G.550 Ligands: NI.12 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.519, E:H.545, H2O.1313, H2O.1315 NI.12: 5 residues within 4Å: Chain E: H.407, H.409, K.490, D.633 Ligands: NI.11 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:H.407, E:H.409, E:D.633, H2O.1314, H2O.1315 NI.13: 5 residues within 4Å: Chain F: H.407, H.409, K.490, D.633 Ligands: NI.14 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.407, F:H.409, F:D.633, H2O.1612, H2O.1613 NI.14: 7 residues within 4Å: Chain F: H.407, K.490, H.492, H.519, H.545, G.550 Ligands: NI.13 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:H.519, F:H.545, H2O.1612, H2O.1615

3 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 6 residues within 4Å: Chain B: R.29, R.67, V.70, P.72, N.127, D.128 No protein-ligand interaction detected (PLIP) MG.10: 6 residues within 4Å: Chain D: R.29, R.67, V.70, P.72, N.127, D.128 No protein-ligand interaction detected (PLIP) MG.15: 6 residues within 4Å: Chain F: R.29, R.67, V.70, P.72, N.127, D.128 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Balasubramanian, A. et al., Structural and functional studies on urease from pigeon pea (Cajanus cajan). Int.J.Biol.Macromol. (2013)

Release Date

2013-06-05

Peptides

urease: ACE
urease: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

urease

urease