SMTL ID : 3la4.1

Crystal structure of the first plant urease from Jack bean (Canavalia ensiformis)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-hexamer

Ligands

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

NI.1: 6 residues within 4Å: Chain A: H.407, H.409, K.490, D.633 Ligands: NI.2, PO4.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.407, A:H.409, A:D.633 NI.2: 7 residues within 4Å: Chain A: K.490, H.492, H.519, H.545, G.550 Ligands: NI.1, PO4.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.519, A:H.545 NI.6: 6 residues within 4Å: Chain B: H.407, H.409, K.490, D.633 Ligands: NI.7, PO4.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.407, B:H.409, B:D.633 NI.7: 7 residues within 4Å: Chain B: K.490, H.492, H.519, H.545, G.550 Ligands: NI.6, PO4.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.519, B:H.545 NI.11: 6 residues within 4Å: Chain C: H.407, H.409, K.490, D.633 Ligands: NI.12, PO4.13 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.407, C:H.409, C:D.633 NI.12: 7 residues within 4Å: Chain C: K.490, H.492, H.519, H.545, G.550 Ligands: NI.11, PO4.13 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.519, C:H.545 NI.16: 6 residues within 4Å: Chain D: H.407, H.409, K.490, D.633 Ligands: NI.17, PO4.18 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:H.407, D:H.409, D:D.633 NI.17: 7 residues within 4Å: Chain D: K.490, H.492, H.519, H.545, G.550 Ligands: NI.16, PO4.18 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:H.519, D:H.545 NI.21: 6 residues within 4Å: Chain E: H.407, H.409, K.490, D.633 Ligands: NI.22, PO4.23 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:H.407, E:H.409, E:D.633 NI.22: 7 residues within 4Å: Chain E: K.490, H.492, H.519, H.545, G.550 Ligands: NI.21, PO4.23 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:H.519, E:H.545 NI.26: 6 residues within 4Å: Chain F: H.407, H.409, K.490, D.633 Ligands: NI.27, PO4.28 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:H.407, F:H.409, F:D.633 NI.27: 7 residues within 4Å: Chain F: K.490, H.492, H.519, H.545, G.550 Ligands: NI.26, PO4.28 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:H.519, F:H.545

12 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 14 residues within 4Å: Chain A: H.407, H.409, A.440, K.490, H.492, H.519, H.545, G.550, D.633, A.636, M.637 Ligands: NI.1, NI.2, PO4.4 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:A.440 Salt bridges: A:H.407, A:H.409, A:H.492, A:H.519, A:H.545 PO4.4: 8 residues within 4Å: Chain A: H.492, E.493, D.494, H.519, G.550, H.593, R.609 Ligands: PO4.3 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.493, A:D.494 Water bridges: A:E.493, A:R.609 Salt bridges: A:H.492, A:H.519, A:H.593, A:R.609 PO4.8: 14 residues within 4Å: Chain B: H.407, H.409, A.440, K.490, H.492, H.519, H.545, G.550, D.633, A.636, M.637 Ligands: NI.6, NI.7, PO4.9 5 PLIP interactions: 5 interactions with chain B Salt bridges: B:H.407, B:H.409, B:H.492, B:H.519, B:H.545 PO4.9: 8 residues within 4Å: Chain B: H.492, E.493, D.494, H.519, G.550, H.593, R.609 Ligands: PO4.8 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.493, B:D.494 Water bridges: B:E.493, B:R.609 Salt bridges: B:H.492, B:H.519, B:H.593, B:R.609 PO4.13: 14 residues within 4Å: Chain C: H.407, H.409, A.440, K.490, H.492, H.519, H.545, G.550, D.633, A.636, M.637 Ligands: NI.11, NI.12, PO4.14 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:A.440 Salt bridges: C:H.407, C:H.409, C:H.492, C:H.519, C:H.545 PO4.14: 8 residues within 4Å: Chain C: H.492, E.493, D.494, H.519, G.550, H.593, R.609 Ligands: PO4.13 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:E.493, C:D.494 Water bridges: C:E.493, C:R.609 Salt bridges: C:H.492, C:H.519, C:H.593, C:R.609 PO4.18: 14 residues within 4Å: Chain D: H.407, H.409, A.440, K.490, H.492, H.519, H.545, G.550, D.633, A.636, M.637 Ligands: NI.16, NI.17, PO4.19 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:A.440 Salt bridges: D:H.407, D:H.409, D:H.492, D:H.519, D:H.545 PO4.19: 8 residues within 4Å: Chain D: H.492, E.493, D.494, H.519, G.550, H.593, R.609 Ligands: PO4.18 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:D.494 Water bridges: D:T.522, D:T.522 Salt bridges: D:H.492, D:H.519, D:H.593, D:R.609 PO4.23: 14 residues within 4Å: Chain E: H.407, H.409, A.440, K.490, H.492, H.519, H.545, G.550, D.633, A.636, M.637 Ligands: NI.21, NI.22, PO4.24 6 PLIP interactions: 6 interactions with chain E Hydrogen bonds: E:A.440 Salt bridges: E:H.407, E:H.409, E:H.492, E:H.519, E:H.545 PO4.24: 8 residues within 4Å: Chain E: H.492, E.493, D.494, H.519, G.550, H.593, R.609 Ligands: PO4.23 7 PLIP interactions: 7 interactions with chain E Hydrogen bonds: E:D.494 Water bridges: E:T.522, E:T.522 Salt bridges: E:H.492, E:H.519, E:H.593, E:R.609 PO4.28: 14 residues within 4Å: Chain F: H.407, H.409, A.440, K.490, H.492, H.519, H.545, G.550, D.633, A.636, M.637 Ligands: NI.26, NI.27, PO4.29 5 PLIP interactions: 5 interactions with chain F Salt bridges: F:H.407, F:H.409, F:H.492, F:H.519, F:H.545 PO4.29: 8 residues within 4Å: Chain F: H.492, E.493, D.494, H.519, G.550, H.593, R.609 Ligands: PO4.28 7 PLIP interactions: 7 interactions with chain F Hydrogen bonds: F:D.494 Water bridges: F:T.522, F:T.522 Salt bridges: F:H.492, F:H.519, F:H.593, F:R.609

6 x ACN: ACETONE(Non-covalent)

ACN.5: 2 residues within 4Å: Chain E: R.222 Ligands: ACN.25 No protein-ligand interaction detected (PLIP) ACN.10: 2 residues within 4Å: Chain D: R.222 Ligands: ACN.20 No protein-ligand interaction detected (PLIP) ACN.15: 2 residues within 4Å: Chain F: R.222 Ligands: ACN.30 No protein-ligand interaction detected (PLIP) ACN.20: 2 residues within 4Å: Chain B: R.222 Ligands: ACN.10 No protein-ligand interaction detected (PLIP) ACN.25: 2 residues within 4Å: Chain A: R.222 Ligands: ACN.5 No protein-ligand interaction detected (PLIP) ACN.30: 2 residues within 4Å: Chain C: R.222 Ligands: ACN.15 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Balasubramanian, A. et al., Crystal structure of the first plant urease from jack bean: 83 years of journey from its first crystal to molecular structure. J.Mol.Biol. (2010)

Release Date

2010-07-28

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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