SMTL ID : 4h9m.1

The first Jack bean urease (Canavalia ensiformis) complex obtained at 1.52 resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.52 Å

Oligo State

homo-trimer

Ligands

6 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, HAE.29 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.407, A:H.409, A:D.633, HAE.29 NI.2: 7 residues within 4Å: Chain A: K.490, H.492, H.519, H.545, G.550 Ligands: NI.1, HAE.29 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.519, A:H.545, HAE.29 NI.33: 6 residues within 4Å: Chain B: H.407, H.409, K.490, D.633 Ligands: NI.34, HAE.61 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.407, B:H.409, B:D.633, HAE.61 NI.34: 7 residues within 4Å: Chain B: K.490, H.492, H.519, H.545, G.550 Ligands: NI.33, HAE.61 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions Metal complexes: B:H.519, B:H.545, HAE.61 NI.65: 6 residues within 4Å: Chain C: H.407, H.409, K.490, D.633 Ligands: NI.66, HAE.93 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:H.407, C:H.409, C:D.633, HAE.93 NI.66: 7 residues within 4Å: Chain C: K.490, H.492, H.519, H.545, G.550 Ligands: NI.65, HAE.93 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Ligand interactions Metal complexes: C:H.519, C:H.545, HAE.93

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

EDO.3: 6 residues within 4Å: Chain A: L.111, F.112, G.113, S.114, L.115 Chain B: R.26 Ligand excluded by PLIP EDO.4: 6 residues within 4Å: Chain A: A.80, V.81, Q.82, T.740, E.742, V.744 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: I.154, S.209, V.210, T.211 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: R.6, K.10, T.86, T.91, N.735 Chain B: F.838, F.840 Ligand excluded by PLIP EDO.7: 2 residues within 4Å: Chain A: P.72, R.835 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: G.217, P.373, M.376, N.377, G.378, V.379 Ligand excluded by PLIP EDO.9: 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.10: 6 residues within 4Å: Chain A: D.361, G.362, G.723, A.759, L.760, R.783 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: T.350, I.353, I.367, V.697, E.698 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: A.280, N.281, E.395, G.396 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: R.26, G.27, V.28 Chain C: D.49 Ligand excluded by PLIP EDO.14: 8 residues within 4Å: Chain A: G.12, L.13, P.743, K.745 Chain C: M.1, L.3, V.8, L.11 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: A.196, G.197, T.198, K.282, Y.283, K.319 Ligand excluded by PLIP EDO.16: 2 residues within 4Å: Chain A: E.480, K.483 Ligand excluded by PLIP EDO.17: 4 residues within 4Å: Chain A: S.473, A.500, D.503, N.504 Ligand excluded by PLIP EDO.18: 1 residues within 4Å: Chain A: S.120 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: R.102, N.104, G.105, E.106 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain A: Y.417, W.728, P.748 Ligand excluded by PLIP EDO.21: 6 residues within 4Å: Chain A: Q.166, G.317 Chain B: L.523, H.593, L.595, F.605 Ligand excluded by PLIP EDO.22: 3 residues within 4Å: Chain A: N.218, V.220, P.231 Ligand excluded by PLIP EDO.23: 4 residues within 4Å: Chain A: L.770, N.775, V.784, E.785 Ligand excluded by PLIP EDO.24: 6 residues within 4Å: Chain A: I.335, L.337, K.360, A.365, S.381, N.382 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain A: D.810, S.813, T.815 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain A: A.440, D.494, H.593 Chain C: G.316, G.317 Ligand excluded by PLIP EDO.27: 2 residues within 4Å: Chain A: E.510, H.511 Ligand excluded by PLIP EDO.28: 7 residues within 4Å: Chain A: G.538, T.540, N.565, R.791, K.792, L.793, T.794 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain A: T.339, G.724, M.725, V.726 Chain B: T.432, Q.449 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain A: R.132, N.297, A.656 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain A: Y.188, V.232, N.233, E.234, L.237 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain B: L.111, F.112, G.113, S.114, L.115 Chain C: R.26 Ligand excluded by PLIP EDO.36: 6 residues within 4Å: Chain B: A.80, V.81, Q.82, T.740, E.742, V.744 Ligand excluded by PLIP EDO.37: 4 residues within 4Å: Chain B: I.154, S.209, V.210, T.211 Ligand excluded by PLIP EDO.38: 7 residues within 4Å: Chain B: R.6, K.10, T.86, T.91, N.735 Chain C: F.838, F.840 Ligand excluded by PLIP EDO.39: 2 residues within 4Å: Chain B: P.72, R.835 Ligand excluded by PLIP EDO.40: 6 residues within 4Å: Chain B: G.217, P.373, M.376, N.377, G.378, V.379 Ligand excluded by PLIP EDO.41: 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.42: 6 residues within 4Å: Chain B: D.361, G.362, G.723, A.759, L.760, R.783 Ligand excluded by PLIP EDO.43: 5 residues within 4Å: Chain B: T.350, I.353, I.367, V.697, E.698 Ligand excluded by PLIP EDO.44: 4 residues within 4Å: Chain B: A.280, N.281, E.395, G.396 Ligand excluded by PLIP EDO.45: 4 residues within 4Å: Chain A: D.49 Chain B: R.26, G.27, V.28 Ligand excluded by PLIP EDO.46: 8 residues within 4Å: Chain A: M.1, L.3, V.8, L.11 Chain B: G.12, L.13, P.743, K.745 Ligand excluded by PLIP EDO.47: 6 residues within 4Å: Chain B: A.196, G.197, T.198, K.282, Y.283, K.319 Ligand excluded by PLIP EDO.48: 2 residues within 4Å: Chain B: E.480, K.483 Ligand excluded by PLIP EDO.49: 4 residues within 4Å: Chain B: S.473, A.500, D.503, N.504 Ligand excluded by PLIP EDO.50: 1 residues within 4Å: Chain B: S.120 Ligand excluded by PLIP EDO.51: 4 residues within 4Å: Chain B: R.102, N.104, G.105, E.106 Ligand excluded by PLIP EDO.52: 3 residues within 4Å: Chain B: Y.417, W.728, P.748 Ligand excluded by PLIP EDO.53: 6 residues within 4Å: Chain B: Q.166, G.317 Chain C: L.523, H.593, L.595, F.605 Ligand excluded by PLIP EDO.54: 3 residues within 4Å: Chain B: N.218, V.220, P.231 Ligand excluded by PLIP EDO.55: 4 residues within 4Å: Chain B: L.770, N.775, V.784, E.785 Ligand excluded by PLIP EDO.56: 6 residues within 4Å: Chain B: I.335, L.337, K.360, A.365, S.381, N.382 Ligand excluded by PLIP EDO.57: 3 residues within 4Å: Chain B: D.810, S.813, T.815 Ligand excluded by PLIP EDO.58: 5 residues within 4Å: Chain A: G.316, G.317 Chain B: A.440, D.494, H.593 Ligand excluded by PLIP EDO.59: 2 residues within 4Å: Chain B: E.510, H.511 Ligand excluded by PLIP EDO.60: 7 residues within 4Å: Chain B: G.538, T.540, N.565, R.791, K.792, L.793, T.794 Ligand excluded by PLIP EDO.62: 6 residues within 4Å: Chain B: T.339, G.724, M.725, V.726 Chain C: T.432, Q.449 Ligand excluded by PLIP EDO.63: 3 residues within 4Å: Chain B: R.132, N.297, A.656 Ligand excluded by PLIP EDO.64: 5 residues within 4Å: Chain B: Y.188, V.232, N.233, E.234, L.237 Ligand excluded by PLIP EDO.67: 6 residues within 4Å: Chain A: R.26 Chain C: L.111, F.112, G.113, S.114, L.115 Ligand excluded by PLIP EDO.68: 6 residues within 4Å: Chain C: A.80, V.81, Q.82, T.740, E.742, V.744 Ligand excluded by PLIP EDO.69: 4 residues within 4Å: Chain C: I.154, S.209, V.210, T.211 Ligand excluded by PLIP EDO.70: 7 residues within 4Å: Chain A: F.838, F.840 Chain C: R.6, K.10, T.86, T.91, N.735 Ligand excluded by PLIP EDO.71: 2 residues within 4Å: Chain C: P.72, R.835 Ligand excluded by PLIP EDO.72: 6 residues within 4Å: Chain C: G.217, P.373, M.376, N.377, G.378, V.379 Ligand excluded by PLIP EDO.73: 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.74: 6 residues within 4Å: Chain C: D.361, G.362, G.723, A.759, L.760, R.783 Ligand excluded by PLIP EDO.75: 5 residues within 4Å: Chain C: T.350, I.353, I.367, V.697, E.698 Ligand excluded by PLIP EDO.76: 4 residues within 4Å: Chain C: A.280, N.281, E.395, G.396 Ligand excluded by PLIP EDO.77: 4 residues within 4Å: Chain B: D.49 Chain C: R.26, G.27, V.28 Ligand excluded by PLIP EDO.78: 8 residues within 4Å: Chain B: M.1, L.3, V.8, L.11 Chain C: G.12, L.13, P.743, K.745 Ligand excluded by PLIP EDO.79: 6 residues within 4Å: Chain C: A.196, G.197, T.198, K.282, Y.283, K.319 Ligand excluded by PLIP EDO.80: 2 residues within 4Å: Chain C: E.480, K.483 Ligand excluded by PLIP EDO.81: 4 residues within 4Å: Chain C: S.473, A.500, D.503, N.504 Ligand excluded by PLIP EDO.82: 1 residues within 4Å: Chain C: S.120 Ligand excluded by PLIP EDO.83: 4 residues within 4Å: Chain C: R.102, N.104, G.105, E.106 Ligand excluded by PLIP EDO.84: 3 residues within 4Å: Chain C: Y.417, W.728, P.748 Ligand excluded by PLIP EDO.85: 6 residues within 4Å: Chain A: L.523, H.593, L.595, F.605 Chain C: Q.166, G.317 Ligand excluded by PLIP EDO.86: 3 residues within 4Å: Chain C: N.218, V.220, P.231 Ligand excluded by PLIP EDO.87: 4 residues within 4Å: Chain C: L.770, N.775, V.784, E.785 Ligand excluded by PLIP EDO.88: 6 residues within 4Å: Chain C: I.335, L.337, K.360, A.365, S.381, N.382 Ligand excluded by PLIP EDO.89: 3 residues within 4Å: Chain C: D.810, S.813, T.815 Ligand excluded by PLIP EDO.90: 5 residues within 4Å: Chain B: G.316, G.317 Chain C: A.440, D.494, H.593 Ligand excluded by PLIP EDO.91: 2 residues within 4Å: Chain C: E.510, H.511 Ligand excluded by PLIP EDO.92: 7 residues within 4Å: Chain C: G.538, T.540, N.565, R.791, K.792, L.793, T.794 Ligand excluded by PLIP EDO.94: 6 residues within 4Å: Chain A: T.432, Q.449 Chain C: T.339, G.724, M.725, V.726 Ligand excluded by PLIP EDO.95: 3 residues within 4Å: Chain C: R.132, N.297, A.656 Ligand excluded by PLIP EDO.96: 5 residues within 4Å: Chain C: Y.188, V.232, N.233, E.234, L.237 Ligand excluded by PLIP

3 x HAE: ACETOHYDROXAMIC ACID(Non-covalent)

HAE.29: 10 residues within 4Å: Chain A: H.407, A.440, K.490, H.492, H.519, H.545, G.550, D.633 Ligands: NI.1, NI.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.633 Water bridges: A:R.609 HAE.61: 10 residues within 4Å: Chain B: H.407, A.440, K.490, H.492, H.519, H.545, G.550, D.633 Ligands: NI.33, NI.34 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.633 Water bridges: B:R.609 HAE.93: 10 residues within 4Å: Chain C: H.407, A.440, K.490, H.492, H.519, H.545, G.550, D.633 Ligands: NI.65, NI.66 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.633 Water bridges: C:R.609

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Begum, A. et al., The first Jack bean urease (Canavalia ensiformis) complex obtained at 1.52 resolution. TO BE PUBLISHED

Release Date

2012-10-24

Peptides

Urease: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Urease

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