SMTL ID : 4zla.1

Bestatin complex structure of leucine aminopeptidase from Helicobacter pylori

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-hexamer

Ligands

12 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: K.264, D.269, D.287, E.348 Ligands: ZN.2, BCT.4, BES.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.269, A:D.287, A:E.348 ZN.2: 6 residues within 4Å: Chain A: D.269, K.276, D.346, E.348 Ligands: ZN.1, BES.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.269, A:D.346, A:D.346, A:E.348 ZN.6: 7 residues within 4Å: Chain B: K.264, D.269, D.287, E.348 Ligands: ZN.7, BCT.9, BES.10 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:D.269, B:D.287, B:E.348 ZN.7: 6 residues within 4Å: Chain B: D.269, K.276, D.346, E.348 Ligands: ZN.6, BES.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.269, B:D.346, B:D.346, B:E.348 ZN.11: 7 residues within 4Å: Chain C: K.264, D.269, D.287, E.348 Ligands: ZN.12, BCT.14, BES.15 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.269, C:D.287, C:E.348 ZN.12: 6 residues within 4Å: Chain C: D.269, K.276, D.346, E.348 Ligands: ZN.11, BES.15 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.269, C:D.346, C:D.346, C:E.348 ZN.16: 7 residues within 4Å: Chain D: K.264, D.269, D.287, E.348 Ligands: ZN.17, BCT.19, BES.20 3 PLIP interactions: 3 interactions with chain D Metal complexes: D:D.269, D:D.287, D:E.348 ZN.17: 6 residues within 4Å: Chain D: D.269, K.276, D.346, E.348 Ligands: ZN.16, BES.20 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.269, D:D.346, D:D.346, D:E.348 ZN.21: 7 residues within 4Å: Chain E: K.264, D.269, D.287, E.348 Ligands: ZN.22, BCT.24, BES.25 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.269, E:D.287, E:E.348 ZN.22: 6 residues within 4Å: Chain E: D.269, K.276, D.346, E.348 Ligands: ZN.21, BES.25 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.269, E:D.346, E:D.346, E:E.348 ZN.26: 7 residues within 4Å: Chain F: K.264, D.269, D.287, E.348 Ligands: ZN.27, BCT.29, BES.30 3 PLIP interactions: 3 interactions with chain F Metal complexes: F:D.269, F:D.287, F:E.348 ZN.27: 6 residues within 4Å: Chain F: D.269, K.276, D.346, E.348 Ligands: ZN.26, BES.30 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.269, F:D.346, F:D.346, F:E.348

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
A

B
B

C
C

D
D

E
E

F
F

Cytosol aminopeptidase

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