SMTL ID : 4xna.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 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: B3K.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, B3K.2

1 x B3K: (3S)-3,7-DIAMINOHEPTANOIC ACID(Non-covalent)

B3K.2: 16 residues within 4Å: Chain A: 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, Q.817 Ligands: ZN.1, MLI.20 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.372, A:Y.372 Hydrogen bonds: A:E.117, A:E.294, A:N.369, A:Y.377, A:Q.817 Salt bridges: A:H.293, A:H.297

4 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:Q.15, A:I.16, A:L.134 NA.4: 4 residues within 4Å: Chain A: S.328, D.329, G.331, R.333 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.329, A:R.333 NA.5: 6 residues within 4Å: Chain A: Y.181, L.182, E.260, G.301, N.302, K.315 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.181, A:E.260, A:G.301, A:K.315 NA.6: 4 residues within 4Å: Chain A: L.547, S.566, L.567, T.570 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.566, A:T.570, A:T.570

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain A: A.527, L.528, W.542, S.559, D.562, A.563, S.566 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.528, A:D.562, A:S.566, A:S.566 Water bridges: A:L.528 GOL.8: 9 residues within 4Å: Chain A: L.285, G.331, S.332, V.335, N.336, H.668, I.671, A.672, T.675 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.332, A:N.336, A:H.668, A:H.668, A:T.675 Water bridges: A:S.327 GOL.9: 3 residues within 4Å: Chain A: N.63, D.64, T.87 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:D.64, A:T.87 Water bridges: A:N.63, A:D.64, A:D.64, A:T.87, A:T.87 GOL.10: 5 residues within 4Å: Chain A: D.448, Y.457, Q.523, P.524, Q.546 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.448, A:Y.450, A:Q.523, A:P.524, A:Q.546 Water bridges: A:Y.540 GOL.11: 4 residues within 4Å: Chain A: L.57, V.58, S.59, W.70 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.58 GOL.12: 6 residues within 4Å: Chain A: P.175, F.176, P.177, R.303, D.408, G.409 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.303, A:D.408 GOL.13: 4 residues within 4Å: Chain A: K.497, T.514, F.515, V.516 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.497, A:V.516 Water bridges: A:N.503, A:N.503 GOL.14: 7 residues within 4Å: Chain A: P.12, D.13, Y.14, L.48, R.49, L.128, R.130 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.13, A:R.49, A:R.130 Water bridges: A:N.51, A:R.130 GOL.15: 3 residues within 4Å: Chain A: R.665, V.666, E.667 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.666, A:E.667, A:E.667

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

MLI.16: 6 residues within 4Å: Chain A: R.637, E.638, T.641, R.682, F.686, A.718 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.686 Hydrogen bonds: A:E.638 Water bridges: A:R.637, A:T.641, A:T.641 Salt bridges: A:R.637, A:R.637, A:R.682 MLI.17: 9 residues within 4Å: Chain A: D.277, F.700, A.703, N.704, N.705, M.706, A.709, K.734, W.735 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.734, A:K.734 MLI.18: 7 residues within 4Å: Chain A: Q.463, R.464, T.465, K.474, Q.475, P.476, A.511 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.476 Hydrogen bonds: A:T.465, A:Q.475 Water bridges: A:Q.463, A:T.465 MLI.19: 2 residues within 4Å: Chain A: E.667, H.668 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:E.667 Hydrogen bonds: A:H.668 Water bridges: A:E.669 Salt bridges: A:H.668 MLI.20: 9 residues within 4Å: Chain A: M.256, G.257, A.258, R.289, V.290, H.293, E.294, Y.377 Ligands: B3K.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.257, A:A.258 Water bridges: A:R.289, A:R.289 Salt bridges: A:R.289, A:H.293

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Addlagatta, A. et al., Crystal Structure of E. coli Aminopeptidase N in complex with L-Beta Homolysin. 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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