SMTL ID : 4xmt.1

Crystal Structure of Met260Ala mutant of E. coli Aminopeptidase N in complex with L-2,3-Diaminopropionic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.294, H.298, E.317 Ligands: DPP.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.294, A:H.298, A:E.317, A:E.317, DPP.2

1 x DPP: DIAMINOPROPANOIC ACID(Non-covalent)

DPP.2: 12 residues within 4Å: Chain A: E.118, A.259, M.260, E.261, H.294, E.295, H.298, K.316, E.317, Y.378 Ligands: ZN.1, GOL.18 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.118, A:Y.378 Water bridges: A:Q.116 Salt bridges: A:H.294, A:H.298, A:K.316

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

NA.3: 3 residues within 4Å: Chain A: S.329, D.330, G.332 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.332, A:R.334 NA.4: 2 residues within 4Å: Chain A: D.449 Ligands: NA.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.449 Water bridges: A:D.449, A:D.449, A:D.449, A:D.449 NA.5: 2 residues within 4Å: Chain A: G.53, G.76 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.76, A:A.77, A:Y.127, A:Y.127 Water bridges: A:E.54, A:D.55 NA.6: 3 residues within 4Å: Chain A: Q.16, I.17, L.135 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.17, A:L.135 NA.7: 3 residues within 4Å: Chain A: D.449, Y.541 Ligands: NA.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.541 Water bridges: A:D.449, A:Q.547 NA.8: 3 residues within 4Å: Chain A: H.768, R.769, F.771 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.771 NA.9: 2 residues within 4Å: Chain A: D.19, D.21 8 PLIP interactions: 8 interactions with chain A Water bridges: A:D.19, A:D.19, A:D.19, A:D.19, A:I.20, A:I.20, A:D.21, A:D.21

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 5 residues within 4Å: Chain A: R.465, T.466, K.475, Q.476, P.477 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.466, A:T.466, A:Q.476 GOL.11: 6 residues within 4Å: Chain A: R.638, E.639, T.642, R.683, F.687, A.719 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.638, A:R.683, A:R.683 Water bridges: A:E.639 GOL.12: 7 residues within 4Å: Chain A: A.528, L.529, W.543, L.551, D.563, A.564, S.567 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.529, A:D.563, A:S.567, A:S.567 Water bridges: A:F.533 GOL.13: 3 residues within 4Å: Chain A: R.666, V.667, E.668 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.667 Water bridges: A:V.667 GOL.14: 6 residues within 4Å: Chain A: W.222, E.289, L.331, V.667, E.668, H.669 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.289, A:V.667 Water bridges: A:N.229, A:H.669 GOL.15: 8 residues within 4Å: Chain A: Y.657, Y.661, R.678, Q.700, A.704, N.705, N.706, D.709 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:R.678, A:R.678, A:N.705, A:N.705, A:N.706, A:D.709 Water bridges: A:Y.657, A:Q.662, A:K.699, A:Q.700, A:N.705, A:D.709, A:D.709, A:D.709 GOL.16: 2 residues within 4Å: Chain A: E.406, D.409 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.406, A:D.409 GOL.17: 6 residues within 4Å: Chain A: D.278, F.701, M.707, A.710, K.735, W.736 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.278, A:F.701, A:K.735, A:W.736 GOL.18: 8 residues within 4Å: Chain A: Q.116, E.118, A.257, N.370, Y.373, Y.378, Q.818 Ligands: DPP.2 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.370, A:Y.378, A:Y.378, A:Q.818 Water bridges: A:Q.116, A:Q.116, A:G.258, A:N.370

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

MLI.19: 6 residues within 4Å: Chain A: A.257, G.258, K.271, Y.272, R.780, R.822 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.258, A:Y.272 Water bridges: A:N.777, A:R.780 Salt bridges: A:K.271, A:R.780, A:R.780, A:R.822

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Addlagatta, A. et al., Crystal Structure of Met260Ala mutant of E. coli Aminopeptidase N in complex with L-2,3-Diaminopropionic acid. 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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