SMTL ID : 4xnd.1

Crystal Structure of E. coli Aminopeptidase N in complex with L-Beta Homotryptophan

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.293, H.297, E.316, Y.377 Ligands: HT7.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.293, A:H.297, A:E.316, A:E.316, HT7.2

1 x HT7: (3S)-3-AMINO-4-(1H-INDOL-3-YL)BUTANOIC ACID(Non-covalent)

HT7.2: 16 residues within 4Å: Chain A: Q.115, E.117, M.256, A.258, M.259, E.260, H.293, E.294, H.297, K.315, E.316, N.369, Y.372, Y.377 Ligands: ZN.1, MLI.41 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.372 Hydrogen bonds: A:E.117, A:A.258 Water bridges: A:Q.115, A:M.256 Salt bridges: A:H.293, A:H.297, A:K.315 pi-Stacking: A:Y.372

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

NA.3: 3 residues within 4Å: Chain A: Q.15, I.16, L.134 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.16, A:L.134, A:L.134 NA.4: 1 residues within 4Å: Ligands: GOL.32 No protein-ligand interaction detected (PLIP) NA.5: 2 residues within 4Å: Chain A: N.395, S.425 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.395, A:N.395 NA.6: 3 residues within 4Å: Chain A: N.340, T.343, E.378 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.343, A:T.343 Water bridges: A:Q.324, A:Q.324 NA.7: 5 residues within 4Å: Chain A: S.328, D.329, G.331, R.333 Ligands: MLI.36 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.331, A:R.333 NA.8: 4 residues within 4Å: Chain A: G.346, A.350, N.619, E.623 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.346, A:E.623 NA.9: 2 residues within 4Å: Chain A: N.63, T.87 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.63, A:T.87, A:T.87 NA.10: 4 residues within 4Å: Chain A: L.547, S.566, L.567, T.570 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.570

22 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 8 residues within 4Å: Chain A: A.527, L.528, L.529, W.542, S.559, D.562, A.563, S.566 Ligand excluded by PLIP GOL.12: 5 residues within 4Å: Chain A: K.4, E.119, D.308, W.309, F.310 Ligand excluded by PLIP GOL.13: 3 residues within 4Å: Chain A: T.68, W.70 Ligands: GOL.15 Ligand excluded by PLIP GOL.14: 4 residues within 4Å: Chain A: E.65, P.66, W.67, T.68 Ligand excluded by PLIP GOL.15: 8 residues within 4Å: Chain A: S.59, V.60, P.66, W.67, T.68, W.70 Ligands: GOL.13, MLI.34 Ligand excluded by PLIP GOL.16: 7 residues within 4Å: Chain A: L.347, N.619, G.787, E.824, P.825, R.828 Ligands: MLI.33 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain A: W.221, E.288, L.330, V.666, E.667, H.668 Ligand excluded by PLIP GOL.18: 9 residues within 4Å: Chain A: Y.656, Y.660, R.677, Q.699, E.702, A.703, N.704, N.705, D.708 Ligand excluded by PLIP GOL.19: 7 residues within 4Å: Chain A: V.618, A.634, T.751, P.753, S.788, N.789 Ligands: MLI.39 Ligand excluded by PLIP GOL.20: 8 residues within 4Å: Chain A: M.256, G.257, K.270, Y.271, R.779, R.821 Ligands: MLI.41, MLI.42 Ligand excluded by PLIP GOL.21: 4 residues within 4Å: Chain A: R.203, E.204, D.244 Ligands: GOL.30 Ligand excluded by PLIP GOL.22: 4 residues within 4Å: Chain A: V.525, Q.545, Q.546, F.549 Ligand excluded by PLIP GOL.23: 1 residues within 4Å: Chain A: N.488 Ligand excluded by PLIP GOL.24: 6 residues within 4Å: Chain A: R.434, S.437, Q.438, Q.471, E.473, Q.475 Ligand excluded by PLIP GOL.25: 3 residues within 4Å: Chain A: N.228, W.232, E.235 Ligand excluded by PLIP GOL.26: 5 residues within 4Å: Chain A: E.240, Y.241, D.242, W.299, R.303 Ligand excluded by PLIP GOL.27: 9 residues within 4Å: Chain A: L.613, T.614, L.615, R.637, T.641, A.679, R.682, F.683 Ligands: MLI.39 Ligand excluded by PLIP GOL.28: 5 residues within 4Å: Chain A: L.285, V.335, N.339, E.611, T.675 Ligand excluded by PLIP GOL.29: 6 residues within 4Å: Chain A: P.12, D.13, Y.14, R.49, L.128, R.130 Ligand excluded by PLIP GOL.30: 7 residues within 4Å: Chain A: N.156, F.176, R.203, D.242, L.243, D.244 Ligands: GOL.21 Ligand excluded by PLIP GOL.31: 2 residues within 4Å: Chain A: D.64, E.65 Ligand excluded by PLIP GOL.32: 1 residues within 4Å: Ligands: NA.4 Ligand excluded by PLIP

14 x MLI: MALONATE ION(Non-functional Binders)

MLI.33: 6 residues within 4Å: Chain A: A.350, I.628, R.828, R.831, Y.832 Ligands: GOL.16 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:I.628 Hydrogen bonds: A:Y.832 Water bridges: A:N.619, A:A.622, A:R.831, A:R.831, A:R.831 Salt bridges: A:R.828, A:R.828, A:R.831 MLI.34: 5 residues within 4Å: Chain A: L.57, V.58, S.59, W.70 Ligands: GOL.15 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.70 Hydrogen bonds: A:L.57 Water bridges: A:L.57 MLI.35: 5 residues within 4Å: Chain A: D.24, D.26, K.29, V.31, R.167 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.29 Salt bridges: A:K.29, A:R.167 MLI.36: 6 residues within 4Å: Chain A: S.328, G.331, S.332, R.333, A.334 Ligands: NA.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.331, A:R.333, A:A.334 Water bridges: A:G.331 MLI.37: 7 residues within 4Å: Chain A: Q.463, R.464, T.465, K.474, Q.475, P.476, A.511 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.465, A:T.465 Water bridges: A:Q.463, A:Q.475 MLI.38: 9 residues within 4Å: Chain A: N.575, R.578, H.579, Q.583, P.584, L.585, E.635, V.636, A.639 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.575 Water bridges: A:Q.583, A:A.639 Salt bridges: A:H.579, A:H.579 MLI.39: 7 residues within 4Å: Chain A: R.637, T.641, R.682, F.686, A.718 Ligands: GOL.19, GOL.27 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.686, A:A.718 Water bridges: A:R.637 Salt bridges: A:R.637, A:R.637, A:R.682 MLI.40: 5 residues within 4Å: Chain A: L.102, Q.107, G.109, F.253, S.773 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.253 Hydrogen bonds: A:G.109, A:S.773 Water bridges: A:Q.107 MLI.41: 10 residues within 4Å: Chain A: M.256, G.257, A.258, R.289, H.293, E.294, Y.377 Ligands: HT7.2, GOL.20, MLI.42 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.257, A:A.258, A:E.294 Water bridges: A:R.289, A:R.289, A:R.289 Salt bridges: A:R.289, A:H.293 MLI.42: 9 residues within 4Å: Chain A: M.256, Y.372, T.373, L.374, Y.377, E.378, R.821 Ligands: GOL.20, MLI.41 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.821 MLI.43: 3 residues within 4Å: Chain A: G.392, E.393, E.394 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.393, A:E.394 Water bridges: A:N.395 MLI.44: 6 residues within 4Å: Chain A: M.551, R.552, R.560, A.594, V.598, D.601 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.601 Salt bridges: A:R.560 MLI.45: 6 residues within 4Å: Chain A: E.235, R.236, F.237, G.238, Q.397, Q.401 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Q.397 Hydrogen bonds: A:R.236, A:Q.401 Water bridges: A:E.235 MLI.46: 4 residues within 4Å: Chain A: D.448, Y.540, K.541, Q.546 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.448, A:Y.540, A:K.541, A:K.541, A:Q.546

Links

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Citation

Addlagatta, A. et al., Crystal Structure of E. coli Aminopeptidase N in complex with L-Beta Homotryptophan. To Be Published

Release Date

2016-03-02

Peptides

Aminopeptidase N: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Aminopeptidase N

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