SMTL ID : 4gy7.1

Crystallographic structure analysis of urease from Jack bean (Canavalia ensiformis) at 1.49 A Resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

homo-trimer

Ligands

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

NI.1: 7 residues within 4Å: Chain A: K.490, H.492, H.519, H.545, G.550 Ligands: NI.2, PO4.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:H.519, A:H.545 NI.2: 6 residues within 4Å: Chain A: H.407, H.409, K.490, D.633 Ligands: NI.1, PO4.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.407, A:H.409, A:D.633 NI.26: 7 residues within 4Å: Chain B: K.490, H.492, H.519, H.545, G.550 Ligands: NI.27, PO4.28 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:H.519, B:H.545 NI.27: 6 residues within 4Å: Chain B: H.407, H.409, K.490, D.633 Ligands: NI.26, PO4.28 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.407, B:H.409, B:D.633 NI.51: 7 residues within 4Å: Chain C: K.490, H.492, H.519, H.545, G.550 Ligands: NI.52, PO4.53 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:H.519, C:H.545 NI.52: 6 residues within 4Å: Chain C: H.407, H.409, K.490, D.633 Ligands: NI.51, PO4.53 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:H.407, C:H.409, C:D.633

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

PO4.3: 13 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 5 PLIP interactions: 5 interactions with chain A Salt bridges: A:H.407, A:H.409, A:H.492, A:H.519, A:H.545 PO4.23: 5 residues within 4Å: Chain A: H.511, H.512, K.767, A.768, D.771 5 PLIP interactions: 5 interactions with chain A Water bridges: A:A.768, A:A.768 Salt bridges: A:H.511, A:H.512, A:K.767 PO4.28: 13 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.26, NI.27 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 PO4.48: 5 residues within 4Å: Chain B: H.511, H.512, K.767, A.768, D.771 5 PLIP interactions: 5 interactions with chain B Water bridges: B:A.768, B:A.768 Salt bridges: B:H.511, B:H.512, B:K.767 PO4.53: 13 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.51, NI.52 5 PLIP interactions: 5 interactions with chain C Salt bridges: C:H.407, C:H.409, C:H.492, C:H.519, C:H.545 PO4.73: 5 residues within 4Å: Chain C: H.511, H.512, K.767, A.768, D.771 5 PLIP interactions: 5 interactions with chain C Water bridges: C:A.768, C:A.768 Salt bridges: C:H.511, C:H.512, C:K.767

39 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain A: N.193, I.194, V.200, V.210, T.211 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: Y.417, W.728 Chain C: P.5 Ligands: ACN.16 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: E.9, M.746, R.747, P.748 Chain B: Q.414 Ligand excluded by PLIP EDO.7: 6 residues within 4Å: Chain A: G.538, T.540, N.565, R.791, K.792, L.793 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: P.178, Y.179, K.247, G.248 Ligands: EDO.12 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: A.196, G.197, K.282, V.314, K.319 Ligand excluded by PLIP EDO.10: 3 residues within 4Å: Chain A: V.118, P.119, S.120 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain A: P.499, A.500, D.503, K.537 Chain C: N.225, K.247 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: Y.179 Chain B: E.530, H.531 Ligands: EDO.8 Ligand excluded by PLIP EDO.13: 3 residues within 4Å: Chain A: Q.692, Y.693, A.786 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain A: Y.417, L.460, P.461, W.728, T.752 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain A: D.49 Chain B: R.26, G.27, V.28 Ligand excluded by PLIP EDO.22: 7 residues within 4Å: Chain A: D.361, G.362, L.702, G.723, A.759, L.760, R.783 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain B: N.193, I.194, V.200, V.210, T.211 Ligand excluded by PLIP EDO.30: 4 residues within 4Å: Chain A: P.5 Chain B: Y.417, W.728 Ligands: ACN.41 Ligand excluded by PLIP EDO.31: 5 residues within 4Å: Chain B: E.9, M.746, R.747, P.748 Chain C: Q.414 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain B: G.538, T.540, N.565, R.791, K.792, L.793 Ligand excluded by PLIP EDO.33: 5 residues within 4Å: Chain B: P.178, Y.179, K.247, G.248 Ligands: EDO.37 Ligand excluded by PLIP EDO.34: 5 residues within 4Å: Chain B: A.196, G.197, K.282, V.314, K.319 Ligand excluded by PLIP EDO.35: 3 residues within 4Å: Chain B: V.118, P.119, S.120 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain A: N.225, K.247 Chain B: P.499, A.500, D.503, K.537 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain B: Y.179 Chain C: E.530, H.531 Ligands: EDO.33 Ligand excluded by PLIP EDO.38: 3 residues within 4Å: Chain B: Q.692, Y.693, A.786 Ligand excluded by PLIP EDO.45: 5 residues within 4Å: Chain B: Y.417, L.460, P.461, W.728, T.752 Ligand excluded by PLIP EDO.46: 4 residues within 4Å: Chain B: D.49 Chain C: R.26, G.27, V.28 Ligand excluded by PLIP EDO.47: 7 residues within 4Å: Chain B: D.361, G.362, L.702, G.723, A.759, L.760, R.783 Ligand excluded by PLIP EDO.54: 5 residues within 4Å: Chain C: N.193, I.194, V.200, V.210, T.211 Ligand excluded by PLIP EDO.55: 4 residues within 4Å: Chain B: P.5 Chain C: Y.417, W.728 Ligands: ACN.66 Ligand excluded by PLIP EDO.56: 5 residues within 4Å: Chain A: Q.414 Chain C: E.9, M.746, R.747, P.748 Ligand excluded by PLIP EDO.57: 6 residues within 4Å: Chain C: G.538, T.540, N.565, R.791, K.792, L.793 Ligand excluded by PLIP EDO.58: 5 residues within 4Å: Chain C: P.178, Y.179, K.247, G.248 Ligands: EDO.62 Ligand excluded by PLIP EDO.59: 5 residues within 4Å: Chain C: A.196, G.197, K.282, V.314, K.319 Ligand excluded by PLIP EDO.60: 3 residues within 4Å: Chain C: V.118, P.119, S.120 Ligand excluded by PLIP EDO.61: 6 residues within 4Å: Chain B: N.225, K.247 Chain C: P.499, A.500, D.503, K.537 Ligand excluded by PLIP EDO.62: 4 residues within 4Å: Chain A: E.530, H.531 Chain C: Y.179 Ligands: EDO.58 Ligand excluded by PLIP EDO.63: 3 residues within 4Å: Chain C: Q.692, Y.693, A.786 Ligand excluded by PLIP EDO.70: 5 residues within 4Å: Chain C: Y.417, L.460, P.461, W.728, T.752 Ligand excluded by PLIP EDO.71: 4 residues within 4Å: Chain A: R.26, G.27, V.28 Chain C: D.49 Ligand excluded by PLIP EDO.72: 7 residues within 4Å: Chain C: D.361, G.362, L.702, G.723, A.759, L.760, R.783 Ligand excluded by PLIP

15 x ACN: ACETONE(Non-covalent)

ACN.14: 3 residues within 4Å: Chain A: K.613, S.813, T.815 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.813 Water bridges: A:D.810 ACN.15: 6 residues within 4Å: Chain A: L.523, H.593, L.595, F.605 Chain C: Q.166, G.317 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:H.593, A:L.595, A:F.605, A:F.605 Hydrogen bonds: C:Q.166 ACN.16: 3 residues within 4Å: Chain A: Y.417, W.728 Ligands: EDO.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.417 ACN.17: 5 residues within 4Å: Chain A: R.439, V.591 Chain C: Q.82, I.738, T.740 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:I.738 Hydrogen bonds: C:T.740, A:R.439 ACN.18: 4 residues within 4Å: Chain A: E.601, D.602 Chain C: Q.166, A.199 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.601 ACN.39: 3 residues within 4Å: Chain B: K.613, S.813, T.815 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.813 Water bridges: B:D.810 ACN.40: 6 residues within 4Å: Chain A: Q.166, G.317 Chain B: L.523, H.593, L.595, F.605 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Q.166 Hydrophobic interactions: B:H.593, B:L.595, B:F.605, B:F.605 ACN.41: 3 residues within 4Å: Chain B: Y.417, W.728 Ligands: EDO.30 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.417 ACN.42: 5 residues within 4Å: Chain A: Q.82, I.738, T.740 Chain B: R.439, V.591 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:I.738 Hydrogen bonds: A:T.740, B:R.439 ACN.43: 4 residues within 4Å: Chain A: Q.166, A.199 Chain B: E.601, D.602 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:E.601 ACN.64: 3 residues within 4Å: Chain C: K.613, S.813, T.815 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.813 Water bridges: C:D.810 ACN.65: 6 residues within 4Å: Chain B: Q.166, G.317 Chain C: L.523, H.593, L.595, F.605 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:Q.166 Hydrophobic interactions: C:H.593, C:L.595, C:F.605, C:F.605 ACN.66: 3 residues within 4Å: Chain C: Y.417, W.728 Ligands: EDO.55 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.417 ACN.67: 5 residues within 4Å: Chain B: Q.82, I.738, T.740 Chain C: R.439, V.591 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:I.738 Hydrogen bonds: B:T.740, C:R.439 ACN.68: 4 residues within 4Å: Chain B: Q.166, A.199 Chain C: E.601, D.602 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:E.601

3 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.19: 6 residues within 4Å: Chain A: A.440, D.494, C.592, H.593 Chain C: G.316, G.317 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:G.317, A:D.494 BME.44: 6 residues within 4Å: Chain A: G.316, G.317 Chain B: A.440, D.494, C.592, H.593 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:G.317, B:D.494 BME.69: 6 residues within 4Å: Chain B: G.316, G.317 Chain C: A.440, D.494, C.592, H.593 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:G.317, C:D.494

6 x NA: SODIUM ION(Non-functional Binders)

NA.24: 4 residues within 4Å: Chain A: P.811 Chain C: D.162, R.163, P.164 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.162 NA.25: 2 residues within 4Å: Chain A: A.828, T.829 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.829, A:T.829 Water bridges: A:Q.657, A:T.829 NA.49: 4 residues within 4Å: Chain A: D.162, R.163, P.164 Chain B: P.811 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.162 NA.50: 2 residues within 4Å: Chain B: A.828, T.829 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.829, B:T.829 Water bridges: B:Q.657, B:T.829 NA.74: 4 residues within 4Å: Chain B: D.162, R.163, P.164 Chain C: P.811 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:P.811 NA.75: 2 residues within 4Å: Chain C: A.828, T.829 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.829, C:T.829 Water bridges: C:Q.657, C:T.829

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Begum, A. et al., Crystallographic structure analysis of urease from Jack bean (Canavalia ensiformis) at 1.49 A Resolution. To be Published

Release Date

2012-11-07

Peptides

Urease: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Urease

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