- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.40 Å
- Oligo State
- monomer
- Ligands
- 1 x ZN: ZINC ION(Non-covalent)
- 1 x 7MK: [(7~{S})-6,6-bis(oxidanyl)-5,7,8,9-tetrahydrobenzo[7]annulen-7-yl]azanium(Non-covalent)
- 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- Water bridges: A:N.528, A:S.529
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.144
- 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:E.142
- 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)
- 3 x CL: CHLORIDE ION(Non-functional Binders)
- 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
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.40 Å
- Oligo State
- monomer
- Ligands
- 1 x ZN: ZINC ION(Non-covalent)
- 1 x 7MK: [(7~{S})-6,6-bis(oxidanyl)-5,7,8,9-tetrahydrobenzo[7]annulen-7-yl]azanium(Non-covalent)
- 10 x GOL: GLYCEROL(Non-functional Binders)
- 8 x NA: SODIUM ION(Non-functional Binders)
- 4 x MLI: MALONATE ION(Non-functional Binders)
- 2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
- 3 x CL: CHLORIDE ION(Non-functional Binders)
- 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