- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.97 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x BCT: BICARBONATE ION(Non-functional Binders)
- 14 x NH4: AMMONIUM ION(Non-functional Binders)
NH4.2: 4 residues within 4Å:- Chain A: G.107, D.108, R.109, Q.110
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:G.107, A:G.107, A:R.109, A:Q.110
- Water bridges: A:D.108
NH4.4: 5 residues within 4Å:- Chain A: K.426, A.427, F.430, Q.510, E.514
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:K.426, A:Q.510
NH4.6: 7 residues within 4Å:- Chain A: T.207, C.313, A.490, A.500, T.501, G.502, R.503
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:T.501, A:T.501, A:G.502, A:R.503, A:R.503
NH4.7: 3 residues within 4Å:- Chain A: N.416, N.417, H.480
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:N.416, A:N.417
- Water bridges: A:E.418
NH4.12: 4 residues within 4Å:- Chain A: L.84, Q.85
- Chain B: L.84, Q.85
2 PLIP interactions:1 interactions with chain A, 1 interactions with chain B- Hydrogen bonds: A:Q.85, B:Q.85
NH4.17: 7 residues within 4Å:- Chain B: P.451, F.452, A.453
- Chain D: F.162, D.163, K.166
- Ligands: EDO.29
2 PLIP interactions:1 interactions with chain D, 1 interactions with chain B- Water bridges: D:K.166
- Hydrogen bonds: B:P.451
NH4.21: 6 residues within 4Å:- Chain C: Q.423, K.426, A.427, F.430, Q.510, E.514
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:K.426, C:Q.510
NH4.22: 4 residues within 4Å:- Chain C: G.107, D.108, R.109, Q.110
6 PLIP interactions:6 interactions with chain C- Hydrogen bonds: C:G.107, C:G.107, C:R.109, C:Q.110, C:Q.110
- Water bridges: C:D.108
NH4.23: 7 residues within 4Å:- Chain C: A.463, G.464, T.465, I.466
- Chain D: V.404, A.405, L.406
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:T.465, C:T.465, C:T.465, C:I.466
NH4.24: 6 residues within 4Å:- Chain C: K.238, V.239, E.240, I.270, L.271, Q.272
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:K.238, C:E.240
NH4.28: 4 residues within 4Å:- Chain D: K.426, A.427, Q.510, E.514
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:K.426, D:Q.510
- Water bridges: D:A.427
NH4.34: 5 residues within 4Å:- Chain E: K.426, A.427, F.430, Q.510, E.514
3 PLIP interactions:3 interactions with chain E- Hydrogen bonds: E:K.426, E:Q.510
- Water bridges: E:A.427
NH4.35: 4 residues within 4Å:- Chain E: G.107, D.108, R.109, Q.110
4 PLIP interactions:4 interactions with chain E- Hydrogen bonds: E:G.107, E:G.107, E:R.109, E:Q.110
NH4.39: 9 residues within 4Å:- Chain F: K.288, D.311, M.312, C.313, G.314, A.315, I.395, A.396, T.397
3 PLIP interactions:3 interactions with chain F- Hydrogen bonds: F:K.288, F:G.314, F:T.397
- 10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.3: 7 residues within 4Å:- Chain A: L.134, G.135, L.151, L.180, L.181, A.182, V.190
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:L.134, A:L.181
EDO.8: 8 residues within 4Å:- Chain A: Y.160, F.162, N.212, D.497, K.498, G.499
- Chain F: P.451, F.452
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:K.498
- Water bridges: A:F.162, A:N.212
EDO.14: 9 residues within 4Å:- Chain B: K.300, D.370, A.371, R.374, L.398, T.399, G.400
- Ligands: BCT.13, MN.19
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:D.370, B:L.398, B:G.400
EDO.15: 5 residues within 4Å:- Chain B: K.426, A.427, F.430, Q.510, E.514
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:Q.510
- Water bridges: B:K.426, B:A.427, B:R.515
EDO.16: 6 residues within 4Å:- Chain B: I.355, V.356, T.357
- Chain D: Y.165, N.216, V.217
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:I.355, B:T.357
- Water bridges: B:T.357, B:T.357
EDO.29: 7 residues within 4Å:- Chain B: P.451, F.452
- Chain D: F.162, N.212, K.498, G.499
- Ligands: NH4.17
3 PLIP interactions:3 interactions with chain D- Hydrogen bonds: D:N.212
- Water bridges: D:R.208, D:K.498
EDO.32: 6 residues within 4Å:- Chain C: L.83, L.84, Q.85
- Chain E: L.83, L.84, Q.85
7 PLIP interactions:4 interactions with chain E, 3 interactions with chain C- Hydrogen bonds: E:L.83, E:Q.85, C:Q.85
- Water bridges: E:Q.85, E:S.86, C:Q.85, C:S.86
EDO.40: 5 residues within 4Å:- Chain F: K.426, A.427, F.430, Q.510, E.514
3 PLIP interactions:3 interactions with chain F- Hydrogen bonds: F:K.426, F:Q.510
- Water bridges: F:R.515
EDO.41: 6 residues within 4Å:- Chain F: D.243, E.244, K.245, P.265, P.266, R.267
3 PLIP interactions:3 interactions with chain F- Hydrogen bonds: F:E.244, F:R.267, F:R.267
EDO.42: 6 residues within 4Å:- Chain A: Y.165, N.216, V.217
- Chain F: I.355, V.356, T.357
2 PLIP interactions:2 interactions with chain F- Hydrogen bonds: F:I.355, F:T.357
- 1 x NO3: NITRATE ION(Non-functional Binders)
- 12 x MN: MANGANESE (II) ION(Non-covalent)
MN.9: 7 residues within 4Å:- Chain A: K.288, D.293, D.311, E.372
- Ligands: BCT.1, MN.10, NA.11
4 PLIP interactions:3 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:D.293, A:D.311, A:E.372, H2O.3
MN.10: 5 residues within 4Å:- Chain A: D.293, K.300, D.370, E.372
- Ligands: MN.9
5 PLIP interactions:3 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:D.293, A:D.370, A:E.372, H2O.3, H2O.9
MN.18: 6 residues within 4Å:- Chain B: K.288, D.293, D.311, E.372
- Ligands: BCT.13, MN.19
5 PLIP interactions:3 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:D.293, B:D.311, B:E.372, H2O.18, H2O.20
MN.19: 6 residues within 4Å:- Chain B: D.293, K.300, D.370, E.372
- Ligands: EDO.14, MN.18
5 PLIP interactions:3 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:D.293, B:D.370, B:E.372, H2O.18, H2O.22
MN.25: 6 residues within 4Å:- Chain C: K.288, D.293, D.311, E.372
- Ligands: BCT.20, MN.26
5 PLIP interactions:3 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:D.293, C:D.311, C:E.372, H2O.33, H2O.35
MN.26: 5 residues within 4Å:- Chain C: D.293, K.300, D.370, E.372
- Ligands: MN.25
5 PLIP interactions:3 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: C:D.293, C:D.370, C:E.372, H2O.35, H2O.39
MN.30: 6 residues within 4Å:- Chain D: K.288, D.293, D.311, E.372
- Ligands: BCT.27, MN.31
5 PLIP interactions:3 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:D.293, D:D.311, D:E.372, H2O.48, H2O.51
MN.31: 5 residues within 4Å:- Chain D: D.293, K.300, D.370, E.372
- Ligands: MN.30
5 PLIP interactions:3 interactions with chain D, 2 Ligand-Water interactions- Metal complexes: D:D.293, D:D.370, D:E.372, H2O.48, H2O.51
MN.36: 6 residues within 4Å:- Chain E: K.288, D.293, D.311, E.372
- Ligands: BCT.33, MN.37
4 PLIP interactions:3 interactions with chain E, 1 Ligand-Water interactions- Metal complexes: E:D.293, E:D.311, E:E.372, H2O.61
MN.37: 5 residues within 4Å:- Chain E: D.293, K.300, D.370, E.372
- Ligands: MN.36
5 PLIP interactions:4 interactions with chain E, 1 Ligand-Water interactions- Metal complexes: E:D.293, E:D.370, E:D.370, E:E.372, H2O.61
MN.44: 5 residues within 4Å:- Chain F: K.288, D.293, D.311, E.372
- Ligands: MN.45
5 PLIP interactions:3 interactions with chain F, 2 Ligand-Water interactions- Metal complexes: F:D.293, F:D.311, F:E.372, H2O.79, H2O.81
MN.45: 5 residues within 4Å:- Chain F: D.293, K.300, D.370, E.372
- Ligands: MN.44
6 PLIP interactions:4 interactions with chain F, 2 Ligand-Water interactions- Metal complexes: F:D.293, F:D.370, F:D.370, F:E.372, H2O.78, H2O.81
- 1 x NA: SODIUM ION(Non-functional Binders)
- 1 x P03: 2-[3-[3-(2-hydroxyethoxy)propoxy]propoxy]ethanol(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Simpson, M.C. et al., Unveiling the Catalytic Mechanism of a Processive Metalloaminopeptidase. Biochemistry (2023)
- Release Date
- 2023-11-15
- Peptides
- Probable cytosol aminopeptidase: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
F
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.97 Å
- Oligo State
- homo-hexamer
- Ligands
- 6 x BCT: BICARBONATE ION(Non-functional Binders)
- 14 x NH4: AMMONIUM ION(Non-functional Binders)
- 10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 1 x NO3: NITRATE ION(Non-functional Binders)
- 12 x MN: MANGANESE (II) ION(Non-covalent)
- 1 x NA: SODIUM ION(Non-functional Binders)
- 1 x P03: 2-[3-[3-(2-hydroxyethoxy)propoxy]propoxy]ethanol(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Simpson, M.C. et al., Unveiling the Catalytic Mechanism of a Processive Metalloaminopeptidase. Biochemistry (2023)
- Release Date
- 2023-11-15
- Peptides
- Probable cytosol aminopeptidase: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
F