- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.57 Å
- Oligo State
- monomer
- Ligands
- 1 x ZN: ZINC ION(Non-covalent)
- 1 x 7ML: [(7~{S})-6,6-bis(oxidanyl)-4-phenyl-5,7,8,9-tetrahydrobenzo[7]annulen-7-yl]azanium(Non-covalent)
- 9 x NA: SODIUM ION(Non-functional Binders)
NA.3: 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.4: 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.5: 1 residues within 4Å:- Chain A: S.529
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:S.529
- Water bridges: A:N.528, A:N.528, A:S.529, A:S.529
NA.6: 3 residues within 4Å:- Chain A: E.144, E.392
- Ligands: NA.8
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:E.144
- Water bridges: A:E.144
NA.7: 3 residues within 4Å:- Chain A: D.473, Y.565, Q.571
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:D.473
- Water bridges: A:Y.565
NA.8: 4 residues within 4Å:- Chain A: E.128, E.392, N.394
- Ligands: NA.6
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:E.392
- Water bridges: A:N.394
NA.9: 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:T.112, A:T.112, A:T.112
NA.10: 2 residues within 4Å:- Chain A: N.532, T.534
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:N.532
NA.11: 1 residues within 4Å:- Chain A: D.473
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:D.473
- Water bridges: A:D.473
- 5 x MLI: MALONATE ION(Non-functional Binders)
MLI.12: 8 residues within 4Å:- Chain A: Y.397, T.398, L.399, Y.402, E.403, R.846
- Ligands: 7ML.2, GOL.38
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:Y.402
- Water bridges: A:L.399
- Salt bridges: A:R.846
MLI.13: 6 residues within 4Å:- Chain A: K.598, L.649, F.650, D.651, I.652
- Ligands: DMS.18
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:D.651
- Water bridges: A:I.652
- Salt bridges: A:K.598
MLI.14: 10 residues within 4Å:- Chain A: A.552, L.553, L.563, W.567, L.572, L.575, S.584, D.587, A.588, S.591
5 PLIP interactions:5 interactions with chain A- Hydrophobic interactions: A:W.567
- Hydrogen bonds: A:L.553, A:S.591
- Water bridges: A:S.584, A:S.584
MLI.15: 3 residues within 4Å:- Chain A: G.417, E.418, E.419
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:E.418, A:E.419
- Water bridges: A:N.420
MLI.16: 6 residues within 4Å:- Chain A: K.29, E.144, W.334, F.335, V.390, M.393
3 PLIP interactions:3 interactions with chain A- Hydrophobic interactions: A:V.390
- Water bridges: A:W.334, A:W.334
- 5 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
DMS.17: 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
DMS.18: 7 residues within 4Å:- Chain A: K.562, E.648, L.649, F.650, D.651, R.856
- Ligands: MLI.13
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:R.856
- Water bridges: A:R.856
- Salt bridges: A:E.648, A:D.651
DMS.19: 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.20: 6 residues within 4Å:- Chain A: D.49, L.50, D.51, K.54, V.56, R.192
1 PLIP interactions:1 interactions with chain A- Salt bridges: A:D.49
DMS.21: 6 residues within 4Å:- Chain A: R.35, A.36, P.37, D.38, H.66, G.67
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:D.38
- Salt bridges: A:D.38
- 4 x CL: CHLORIDE ION(Non-functional Binders)
CL.22: 6 residues within 4Å:- Chain A: V.236, D.237, N.240, A.275, S.294, L.298
Ligand excluded by PLIPCL.23: 5 residues within 4Å:- Chain A: L.638, T.639, L.640, R.662, R.707
Ligand excluded by PLIPCL.24: 3 residues within 4Å:- Chain A: A.820, E.821, D.822
Ligand excluded by PLIPCL.25: 3 residues within 4Å:- Chain A: D.51, A.52, Q.53
Ligand excluded by PLIP- 14 x GOL: GLYCEROL(Non-functional Binders)
GOL.26: 7 residues within 4Å:- Chain A: W.246, N.253, E.313, L.355, V.691, E.692, H.693
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:E.313, A:H.693
- Water bridges: A:N.253, A:H.693
GOL.27: 10 residues within 4Å:- Chain A: Y.681, Y.685, Q.686, R.702, Q.724, E.727, A.728, N.729, N.730, D.733
10 PLIP interactions:10 interactions with chain A- Hydrogen bonds: A:Y.681, A:R.702, A:R.702, A:N.729, A:N.729, A:N.730, A:D.733, A:D.733
- Water bridges: A:Q.724, A:N.729
GOL.28: 8 residues within 4Å:- Chain A: D.302, F.725, A.728, 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.29: 4 residues within 4Å:- Chain A: T.93, W.95, K.96, E.97
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:W.95, A:W.95
GOL.30: 6 residues within 4Å:- Chain A: L.82, V.83, S.84, V.85, W.95, E.97
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:V.83
- Water bridges: A:V.85
GOL.31: 6 residues within 4Å:- Chain A: D.79, L.80, K.81, E.118, I.119, S.120
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:E.118, A:I.119, A:S.120
- Water bridges: A:S.120
GOL.32: 3 residues within 4Å:- Chain A: D.89, E.90, P.91
No protein-ligand interaction detected (PLIP)GOL.33: 11 residues within 4Å:- Chain A: S.133, G.134, D.135, A.136, F.215, D.237, V.274, A.275, V.276, D.277, F.278
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:S.133, A:D.277, A:D.277
- Water bridges: A:D.237
GOL.34: 5 residues within 4Å:- Chain A: T.493, P.494, D.495, Q.496, A.497
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:A.497
GOL.35: 7 residues within 4Å:- Chain A: Q.463, Q.488, R.489, T.490, K.499, Q.500, P.501
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:T.490, A:Q.500
- Water bridges: A:R.489
GOL.36: 9 residues within 4Å:- Chain A: R.314, H.318, V.345, D.348, Q.349, N.365, E.403
- Ligands: 7ML.2, GOL.38
13 PLIP interactions:13 interactions with chain A- Hydrogen bonds: A:R.314, A:D.348, A:D.348, A:Q.349
- Water bridges: A:D.348, A:Q.349, A:N.365, A:N.365, A:N.365, A:N.365, A:E.403, A:E.403, A:E.403
GOL.37: 6 residues within 4Å:- Chain A: L.372, N.644, G.812, E.849, P.850, R.853
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:N.644
- Water bridges: A:N.644, A:R.853, A:R.853, A:R.853, A:R.853
GOL.38: 8 residues within 4Å:- Chain A: G.282, Y.296, R.314, V.315, E.403
- Ligands: 7ML.2, MLI.12, GOL.36
9 PLIP interactions:9 interactions with chain A- Hydrogen bonds: A:G.282, A:G.282, A:R.314, A:R.314
- Water bridges: A:K.295, A:Y.296, A:D.311, A:E.403, A:E.403
GOL.39: 9 residues within 4Å:- Chain A: V.643, A.659, R.662, T.776, S.777, P.778, S.813, N.814, A.816
1 PLIP interactions:1 interactions with chain A- Water bridges: A:T.776
- 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 1.57 Å
- Oligo State
- monomer
- Ligands
- 1 x ZN: ZINC ION(Non-covalent)
- 1 x 7ML: [(7~{S})-6,6-bis(oxidanyl)-4-phenyl-5,7,8,9-tetrahydrobenzo[7]annulen-7-yl]azanium(Non-covalent)
- 9 x NA: SODIUM ION(Non-functional Binders)
- 5 x MLI: MALONATE ION(Non-functional Binders)
- 5 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
- 4 x CL: CHLORIDE ION(Non-functional Binders)
- 14 x GOL: GLYCEROL(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