- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.90 Å
- Oligo State
- homo-hexamer
- Ligands
- 12 x ZN: ZINC ION(Non-covalent)
- 6 x NA: SODIUM ION(Non-functional Binders)
NA.3: 3 residues within 4Å:- Chain A: A.467, G.468, Y.471
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:Y.471, A:Y.471
- Water bridges: A:E.384
NA.8: 3 residues within 4Å:- Chain B: A.467, G.468, Y.471
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:Y.471, B:Y.471
NA.13: 3 residues within 4Å:- Chain C: A.467, G.468, Y.471
2 PLIP interactions:2 interactions with chain C- Hydrogen bonds: C:G.468, C:Y.471
NA.18: 3 residues within 4Å:- Chain D: A.467, G.468, Y.471
2 PLIP interactions:2 interactions with chain D- Hydrogen bonds: D:G.468, D:Y.471
NA.23: 3 residues within 4Å:- Chain E: A.467, G.468, Y.471
2 PLIP interactions:2 interactions with chain E- Hydrogen bonds: E:G.468, E:Y.471
NA.28: 3 residues within 4Å:- Chain F: A.467, G.468, Y.471
3 PLIP interactions:3 interactions with chain F- Hydrogen bonds: F:Y.471, F:Y.471
- Water bridges: F:T.283
- 6 x BCT: BICARBONATE ION(Non-functional Binders)
BCT.4: 9 residues within 4Å:- Chain A: K.264, D.346, A.347, E.348, G.349, R.350, L.374
- Ligands: ZN.1, BES.5
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:K.264, A:R.350, A:R.350
BCT.9: 9 residues within 4Å:- Chain B: K.264, D.346, A.347, E.348, G.349, R.350, L.374
- Ligands: ZN.6, BES.10
3 PLIP interactions:3 interactions with chain B- Hydrogen bonds: B:K.264, B:R.350, B:R.350
BCT.14: 9 residues within 4Å:- Chain C: K.264, D.346, A.347, E.348, G.349, R.350, L.374
- Ligands: ZN.11, BES.15
4 PLIP interactions:4 interactions with chain C- Hydrogen bonds: C:E.348, C:G.349, C:R.350, C:L.374
BCT.19: 9 residues within 4Å:- Chain D: K.264, D.346, A.347, E.348, G.349, R.350, L.374
- Ligands: ZN.16, BES.20
4 PLIP interactions:4 interactions with chain D- Hydrogen bonds: D:D.346, D:E.348, D:G.349, D:R.350
BCT.24: 9 residues within 4Å:- Chain E: K.264, D.346, A.347, E.348, G.349, R.350, L.374
- Ligands: ZN.21, BES.25
5 PLIP interactions:5 interactions with chain E- Hydrogen bonds: E:E.348, E:G.349, E:R.350, E:R.350, E:R.350
BCT.29: 9 residues within 4Å:- Chain F: K.264, D.346, A.347, E.348, G.349, R.350, L.374
- Ligands: ZN.26, BES.30
3 PLIP interactions:3 interactions with chain F- Hydrogen bonds: F:K.264, F:R.350, F:R.350
- 6 x BES: 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID(Non-covalent)
BES.5: 18 residues within 4Å:- Chain A: K.264, D.269, K.276, M.284, D.287, N.344, D.346, E.348, R.350, T.373, L.374, T.375, G.376, I.434, A.467
- Ligands: ZN.1, ZN.2, BCT.4
9 PLIP interactions:9 interactions with chain A- Hydrophobic interactions: A:D.346, A:I.434, A:A.467
- Hydrogen bonds: A:K.276, A:T.373, A:L.374, A:G.376, A:A.377
- Water bridges: A:T.373
BES.10: 18 residues within 4Å:- Chain B: K.264, D.269, K.276, M.284, D.287, N.344, D.346, E.348, R.350, T.373, L.374, T.375, G.376, I.434, A.467
- Ligands: ZN.6, ZN.7, BCT.9
7 PLIP interactions:7 interactions with chain B- Hydrophobic interactions: B:I.434, B:A.467
- Hydrogen bonds: B:K.276, B:T.373, B:L.374, B:G.376
- Water bridges: B:A.377
BES.15: 18 residues within 4Å:- Chain C: K.264, D.269, K.276, M.284, D.287, N.344, D.346, E.348, R.350, T.373, L.374, T.375, G.376, I.434, A.467
- Ligands: ZN.11, ZN.12, BCT.14
8 PLIP interactions:8 interactions with chain C- Hydrophobic interactions: C:I.434, C:A.467
- Hydrogen bonds: C:K.276, C:T.373, C:L.374, C:G.376, C:A.377
- Water bridges: C:K.276
BES.20: 17 residues within 4Å:- Chain D: K.264, D.269, K.276, M.284, D.287, D.346, E.348, R.350, T.373, L.374, T.375, G.376, I.434, A.467
- Ligands: ZN.16, ZN.17, BCT.19
7 PLIP interactions:7 interactions with chain D- Hydrophobic interactions: D:I.434, D:A.467
- Hydrogen bonds: D:K.276, D:T.373, D:L.374, D:G.376
- Water bridges: D:A.377
BES.25: 18 residues within 4Å:- Chain E: K.264, D.269, K.276, M.284, D.287, N.344, D.346, E.348, R.350, T.373, L.374, T.375, G.376, I.434, A.467
- Ligands: ZN.21, ZN.22, BCT.24
7 PLIP interactions:7 interactions with chain E- Hydrophobic interactions: E:I.434, E:A.467
- Hydrogen bonds: E:K.276, E:T.373, E:L.374, E:G.376, E:A.377
BES.30: 18 residues within 4Å:- Chain F: K.264, D.269, K.276, M.284, D.287, N.344, D.346, E.348, R.350, T.373, L.374, T.375, G.376, I.434, A.467
- Ligands: ZN.26, ZN.27, BCT.29
7 PLIP interactions:7 interactions with chain F- Hydrophobic interactions: F:I.434, F:A.467
- Hydrogen bonds: F:K.276, F:T.373, F:L.374, F:G.376, F:A.377
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Modak, J.K. et al., Structural basis for substrate specificity of Helicobacter pylori M17 aminopeptidase. Biochimie (2016)
- Release Date
- 2015-12-23
- Peptides
- 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 1.90 Å
- Oligo State
- homo-hexamer
- Ligands
- 12 x ZN: ZINC ION(Non-covalent)
- 6 x NA: SODIUM ION(Non-functional Binders)
- 6 x BCT: BICARBONATE ION(Non-functional Binders)
- 6 x BES: 2-(3-AMINO-2-HYDROXY-4-PHENYL-BUTYRYLAMINO)-4-METHYL-PENTANOIC ACID(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Modak, J.K. et al., Structural basis for substrate specificity of Helicobacter pylori M17 aminopeptidase. Biochimie (2016)
- Release Date
- 2015-12-23
- Peptides
- Cytosol aminopeptidase: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
F