SMTL ID : 5mfr.1

The crystal structure of E. coli Aminopeptidase N in complex with 7-amino-5,7,8,9-tetrahydrobenzocyclohepten-6-one

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.318, H.322, E.341, Y.402 Ligands: 7MK.2, GOL.11 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.318, A:H.322, A:E.341, A:E.341

1 x 7MK: [(7~{S})-6,6-bis(oxidanyl)-5,7,8,9-tetrahydrobenzo[7]annulen-7-yl]azanium(Non-covalent)

7MK.2: 18 residues within 4Å: Chain A: E.142, M.281, G.282, A.283, M.284, E.285, H.318, E.319, H.322, K.340, E.341, Y.397, Y.402, R.846 Ligands: ZN.1, GOL.11, MLI.21, MLI.22 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:M.281, A:Y.397, A:Y.397, A:Y.402 Hydrogen bonds: A:E.142, A:E.319, A:K.340, A:Y.402 Water bridges: A:Q.140, A:E.319

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: L.372, N.644, G.812, E.849, P.850, R.853 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.644, A:G.812, A:G.812 GOL.4: 7 residues within 4Å: Chain A: W.246, N.253, E.313, L.355, V.691, E.692, H.693 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.313, A:V.691, A:H.693 Water bridges: A:N.253, A:H.693 GOL.5: 7 residues within 4Å: Chain A: D.302, F.725, M.731, A.734, Y.756, K.759, W.760 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.759, A:W.760 Water bridges: A:D.302 GOL.6: 2 residues within 4Å: Chain A: R.690, E.692 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.690, A:E.692 GOL.7: 6 residues within 4Å: Chain A: D.79, L.80, K.81, E.118, I.119, S.120 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.120 Water bridges: A:L.80, A:K.81, A:K.81, A:S.120, A:S.120 GOL.8: 7 residues within 4Å: Chain A: Q.463, Q.488, R.489, T.490, K.499, Q.500, P.501 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.490, A:Q.500 Water bridges: A:R.489, A:R.489 GOL.9: 3 residues within 4Å: Chain A: T.93, W.95, K.96 1 PLIP interactions: 1 interactions with chain A Water bridges: A:W.95 GOL.10: 5 residues within 4Å: Chain A: T.493, P.494, D.495, Q.496, A.497 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.493, A:A.497 GOL.11: 15 residues within 4Å: Chain A: E.142, M.281, A.283, M.284, E.285, H.318, E.319, H.322, K.340, E.341, Y.397, Y.402 Ligands: ZN.1, 7MK.2, MLI.21 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.341, A:Y.402 Water bridges: A:Q.140 GOL.12: 6 residues within 4Å: Chain A: K.562, E.648, L.649, F.650, D.651, R.856 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.648, A:F.650, A:D.651 Water bridges: A:K.562, A:K.562, A:E.648, A:L.649

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

NA.13: 4 residues within 4Å: Chain A: S.353, D.354, G.356, R.358 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.354, A:R.358 NA.14: 3 residues within 4Å: Chain A: H.792, R.793, F.795 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.795, A:F.795 NA.15: 1 residues within 4Å: Chain A: S.529 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.529 Water bridges: A:N.528 NA.16: 1 residues within 4Å: Chain A: D.473 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.473, A:D.473 NA.17: 2 residues within 4Å: Chain A: E.144, E.392 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.392 Water bridges: A:E.144, A:N.394 NA.18: 4 residues within 4Å: Chain A: Q.62, N.88, F.111, T.112 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.88, A:T.112 Water bridges: A:T.112 NA.19: 3 residues within 4Å: Chain A: D.473, Y.565, Q.571 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.473 Water bridges: A:D.473, A:Y.565, A:Q.571 NA.20: 4 residues within 4Å: Chain A: E.142, M.281, N.394, Q.842 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.842 Water bridges: A:Q.842

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

MLI.21: 9 residues within 4Å: Chain A: G.282, A.283, Y.296, V.315, H.318, E.319 Ligands: 7MK.2, GOL.11, MLI.22 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.315 Hydrogen bonds: A:Y.296, A:E.319, A:E.319 Water bridges: A:Y.296, A:H.318, A:H.318 Salt bridges: A:H.318 MLI.22: 8 residues within 4Å: Chain A: Y.397, T.398, L.399, Y.402, E.403, R.846 Ligands: 7MK.2, MLI.21 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.402 Water bridges: A:L.399 Salt bridges: A:R.846 MLI.23: 6 residues within 4Å: Chain A: K.29, E.144, W.334, F.335, V.390, M.393 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:K.29, A:V.390, A:M.393 Water bridges: A:W.334, A:W.334 Salt bridges: A:K.29 MLI.24: 7 residues within 4Å: Chain A: D.49, L.50, D.51, K.54, T.55, V.56, R.192 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.56 Hydrogen bonds: A:D.49, A:D.49 Water bridges: A:K.54

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.25: 6 residues within 4Å: Chain A: T.414, L.415, L.416, G.417, N.528, V.530 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.528 DMS.26: 6 residues within 4Å: Chain A: T.414, A.507, V.530, C.555, E.556, S.558 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.556

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.27: 6 residues within 4Å: Chain A: V.236, D.237, N.240, A.275, S.294, L.298 Ligand excluded by PLIP CL.28: 2 residues within 4Å: Chain A: N.581, D.582 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain A: D.51, A.52, Q.53 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Peng, G. et al., Insight into the remarkable affinity and selectivity of the aminobenzosuberone scaffold for the M1 aminopeptidases family based on structure analysis. Proteins (2017)

Release Date

2017-04-19

Peptides

Aminopeptidase N: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Aminopeptidase N

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