SMTL ID : 2j9a.1

blLAP in Complex with Microginin FR1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.73 Å

Oligo State

homo-hexamer

Ligands

6 x ALA- MLE- TYR- TYR: MICROGININ FR1(Non-covalent)

ALA-MLE-TYR-TYR.1: 16 residues within 4Å: Chain A: K.262, D.332, A.333, R.336, L.360, T.361, G.362, A.363, I.366, I.421, G.422, Y.424, R.425 Chain B: R.425 Ligands: AHY.10, ALA-MLE-TYR-TYR.11 11 PLIP interactions: 10 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.333, A:I.421, A:I.421, A:R.425 Hydrogen bonds: A:L.360, A:G.362, A:G.422, A:G.422, B:R.425 Water bridges: A:E.334, A:A.363 ALA-MLE-TYR-TYR.11: 16 residues within 4Å: Chain A: R.425 Chain B: K.262, D.332, A.333, R.336, L.360, T.361, G.362, A.363, I.366, I.421, G.422, Y.424, R.425 Ligands: ALA-MLE-TYR-TYR.1, AHY.20 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:A.333, B:I.421, B:I.421, B:R.425 Hydrogen bonds: B:D.332, B:G.362, B:G.422, A:R.425 Water bridges: B:E.334, B:A.363, B:Y.424, B:T.431, B:T.431 ALA-MLE-TYR-TYR.21: 16 residues within 4Å: Chain C: K.262, D.332, A.333, R.336, L.360, T.361, G.362, A.363, I.366, I.421, G.422, Y.424, R.425 Chain E: R.425 Ligands: AHY.30, ALA-MLE-TYR-TYR.41 13 PLIP interactions: 12 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: C:A.333, C:I.421, C:I.421, C:R.425 Hydrogen bonds: C:D.332, C:G.362, C:G.422, E:R.425 Water bridges: C:E.334, C:A.363, C:Y.424, C:T.431, C:T.431 ALA-MLE-TYR-TYR.31: 16 residues within 4Å: Chain D: K.262, D.332, A.333, R.336, L.360, T.361, G.362, A.363, I.366, I.421, G.422, Y.424, R.425 Chain F: R.425 Ligands: AHY.40, ALA-MLE-TYR-TYR.51 11 PLIP interactions: 1 interactions with chain F, 10 interactions with chain D Hydrogen bonds: F:R.425, D:L.360, D:G.362, D:G.422, D:G.422 Hydrophobic interactions: D:A.333, D:I.421, D:I.421, D:R.425 Water bridges: D:E.334, D:A.363 ALA-MLE-TYR-TYR.41: 16 residues within 4Å: Chain C: R.425 Chain E: K.262, D.332, A.333, R.336, L.360, T.361, G.362, A.363, I.366, I.421, G.422, Y.424, R.425 Ligands: ALA-MLE-TYR-TYR.21, AHY.50 11 PLIP interactions: 10 interactions with chain E, 1 interactions with chain C Hydrophobic interactions: E:A.333, E:I.421, E:I.421, E:R.425 Hydrogen bonds: E:L.360, E:G.362, E:G.422, E:G.422, C:R.425 Water bridges: E:E.334, E:A.363 ALA-MLE-TYR-TYR.51: 16 residues within 4Å: Chain D: R.425 Chain F: K.262, D.332, A.333, R.336, L.360, T.361, G.362, A.363, I.366, I.421, G.422, Y.424, R.425 Ligands: ALA-MLE-TYR-TYR.31, AHY.60 13 PLIP interactions: 12 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: F:A.333, F:I.421, F:I.421, F:R.425 Hydrogen bonds: F:D.332, F:G.362, F:G.422, D:R.425 Water bridges: F:E.334, F:A.363, F:Y.424, F:T.431, F:T.431

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 4 residues within 4Å: Chain A: A.333, G.335, R.336, L.360 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain B: A.333, G.335, R.336, L.360 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain C: A.333, G.335, R.336, L.360 Ligand excluded by PLIP CL.32: 4 residues within 4Å: Chain D: A.333, G.335, R.336, L.360 Ligand excluded by PLIP CL.42: 4 residues within 4Å: Chain E: A.333, G.335, R.336, L.360 Ligand excluded by PLIP CL.52: 4 residues within 4Å: Chain F: A.333, G.335, R.336, L.360 Ligand excluded by PLIP

18 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 6 residues within 4Å: Chain A: A.48, W.82, E.87, N.88, A.91, P.461 Ligand excluded by PLIP MPD.4: 8 residues within 4Å: Chain A: H.233, Y.234, K.235, P.244, N.295, I.296, V.297, F.349 Ligand excluded by PLIP MPD.5: 7 residues within 4Å: Chain A: P.44, L.46, T.51, R.52 Chain F: Q.99, D.102, L.103 Ligand excluded by PLIP MPD.13: 6 residues within 4Å: Chain B: A.48, W.82, E.87, N.88, A.91, P.461 Ligand excluded by PLIP MPD.14: 8 residues within 4Å: Chain B: H.233, Y.234, K.235, P.244, N.295, I.296, V.297, F.349 Ligand excluded by PLIP MPD.15: 7 residues within 4Å: Chain B: P.44, L.46, T.51, R.52 Chain E: Q.99, D.102, L.103 Ligand excluded by PLIP MPD.23: 6 residues within 4Å: Chain C: A.48, W.82, E.87, N.88, A.91, P.461 Ligand excluded by PLIP MPD.24: 8 residues within 4Å: Chain C: H.233, Y.234, K.235, P.244, N.295, I.296, V.297, F.349 Ligand excluded by PLIP MPD.25: 7 residues within 4Å: Chain C: P.44, L.46, T.51, R.52 Chain D: Q.99, D.102, L.103 Ligand excluded by PLIP MPD.33: 6 residues within 4Å: Chain D: A.48, W.82, E.87, N.88, A.91, P.461 Ligand excluded by PLIP MPD.34: 8 residues within 4Å: Chain D: H.233, Y.234, K.235, P.244, N.295, I.296, V.297, F.349 Ligand excluded by PLIP MPD.35: 7 residues within 4Å: Chain C: Q.99, D.102, L.103 Chain D: P.44, L.46, T.51, R.52 Ligand excluded by PLIP MPD.43: 6 residues within 4Å: Chain E: A.48, W.82, E.87, N.88, A.91, P.461 Ligand excluded by PLIP MPD.44: 8 residues within 4Å: Chain E: H.233, Y.234, K.235, P.244, N.295, I.296, V.297, F.349 Ligand excluded by PLIP MPD.45: 7 residues within 4Å: Chain B: Q.99, D.102, L.103 Chain E: P.44, L.46, T.51, R.52 Ligand excluded by PLIP MPD.53: 6 residues within 4Å: Chain F: A.48, W.82, E.87, N.88, A.91, P.461 Ligand excluded by PLIP MPD.54: 8 residues within 4Å: Chain F: H.233, Y.234, K.235, P.244, N.295, I.296, V.297, F.349 Ligand excluded by PLIP MPD.55: 7 residues within 4Å: Chain A: Q.99, D.102, L.103 Chain F: P.44, L.46, T.51, R.52 Ligand excluded by PLIP

12 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.6: 9 residues within 4Å: Chain A: Q.79, N.81, W.398 Chain B: T.377, R.399, M.400, P.401, L.402, F.403 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.402 Water bridges: B:R.399 DMS.7: 4 residues within 4Å: Chain A: V.317, R.319 Chain E: L.133, N.176 No protein-ligand interaction detected (PLIP) DMS.16: 9 residues within 4Å: Chain A: T.377, R.399, M.400, P.401, L.402, F.403 Chain B: Q.79, N.81, W.398 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.402 Water bridges: A:R.399 DMS.17: 4 residues within 4Å: Chain B: V.317, R.319 Chain F: L.133, N.176 No protein-ligand interaction detected (PLIP) DMS.26: 9 residues within 4Å: Chain C: Q.79, N.81, W.398 Chain E: T.377, R.399, M.400, P.401, L.402, F.403 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:L.402 Water bridges: E:R.399 DMS.27: 4 residues within 4Å: Chain B: L.133, N.176 Chain C: V.317, R.319 No protein-ligand interaction detected (PLIP) DMS.36: 9 residues within 4Å: Chain D: Q.79, N.81, W.398 Chain F: T.377, R.399, M.400, P.401, L.402, F.403 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:L.402 Water bridges: F:R.399 DMS.37: 4 residues within 4Å: Chain A: L.133, N.176 Chain D: V.317, R.319 No protein-ligand interaction detected (PLIP) DMS.46: 9 residues within 4Å: Chain C: T.377, R.399, M.400, P.401, L.402, F.403 Chain E: Q.79, N.81, W.398 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:L.402 Water bridges: C:R.399 DMS.47: 4 residues within 4Å: Chain D: L.133, N.176 Chain E: V.317, R.319 No protein-ligand interaction detected (PLIP) DMS.56: 9 residues within 4Å: Chain D: T.377, R.399, M.400, P.401, L.402, F.403 Chain F: Q.79, N.81, W.398 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.402 Water bridges: D:R.399 DMS.57: 4 residues within 4Å: Chain C: L.133, N.176 Chain F: V.317, R.319 No protein-ligand interaction detected (PLIP)

12 x ZN: ZINC ION(Non-covalent)

ZN.8: 5 residues within 4Å: Chain A: D.255, D.332, E.334 Ligands: ZN.9, AHY.10 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.255, A:D.332, A:D.332, A:E.334 ZN.9: 6 residues within 4Å: Chain A: K.250, D.255, D.273, E.334 Ligands: ZN.8, AHY.10 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.255, A:D.273, A:D.273, A:E.334 ZN.18: 5 residues within 4Å: Chain B: D.255, D.332, E.334 Ligands: ZN.19, AHY.20 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.255, B:D.332, B:D.332, B:E.334 ZN.19: 6 residues within 4Å: Chain B: K.250, D.255, D.273, E.334 Ligands: ZN.18, AHY.20 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.255, B:D.273, B:D.273, B:E.334 ZN.28: 5 residues within 4Å: Chain C: D.255, D.332, E.334 Ligands: ZN.29, AHY.30 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.255, C:D.332, C:D.332, C:E.334 ZN.29: 6 residues within 4Å: Chain C: K.250, D.255, D.273, E.334 Ligands: ZN.28, AHY.30 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.255, C:D.273, C:D.273, C:E.334 ZN.38: 5 residues within 4Å: Chain D: D.255, D.332, E.334 Ligands: ZN.39, AHY.40 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.255, D:D.332, D:D.332, D:E.334 ZN.39: 6 residues within 4Å: Chain D: K.250, D.255, D.273, E.334 Ligands: ZN.38, AHY.40 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.255, D:D.273, D:D.273, D:E.334 ZN.48: 5 residues within 4Å: Chain E: D.255, D.332, E.334 Ligands: ZN.49, AHY.50 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.255, E:D.332, E:D.332, E:E.334 ZN.49: 6 residues within 4Å: Chain E: K.250, D.255, D.273, E.334 Ligands: ZN.48, AHY.50 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.255, E:D.273, E:D.273, E:E.334 ZN.58: 5 residues within 4Å: Chain F: D.255, D.332, E.334 Ligands: ZN.59, AHY.60 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.255, F:D.332, F:D.332, F:E.334 ZN.59: 6 residues within 4Å: Chain F: K.250, D.255, D.273, E.334 Ligands: ZN.58, AHY.60 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.255, F:D.273, F:D.273, F:E.334

6 x AHY: (2S,3R)-3-AMINO-2-HYDROXYDECANOIC ACID(Non-covalent)

AHY.10: 17 residues within 4Å: Chain A: K.250, D.255, K.262, M.270, D.273, D.332, E.334, T.359, L.360, G.362, D.365, A.451 Chain B: R.425 Ligands: ALA-MLE-TYR-TYR.1, ALA-MLE-TYR-TYR.1, ZN.8, ZN.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.365 Hydrogen bonds: A:K.262, A:T.359 Water bridges: A:E.334 AHY.20: 17 residues within 4Å: Chain A: R.425 Chain B: K.250, D.255, K.262, M.270, D.273, D.332, E.334, T.359, L.360, G.362, D.365, A.451 Ligands: ALA-MLE-TYR-TYR.11, ALA-MLE-TYR-TYR.11, ZN.18, ZN.19 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:D.365 Hydrogen bonds: B:K.262, B:T.359 Water bridges: B:E.334 AHY.30: 17 residues within 4Å: Chain C: K.250, D.255, K.262, M.270, D.273, D.332, E.334, T.359, L.360, G.362, D.365, A.451 Chain E: R.425 Ligands: ALA-MLE-TYR-TYR.21, ALA-MLE-TYR-TYR.21, ZN.28, ZN.29 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:D.365 Hydrogen bonds: C:K.262, C:T.359 Water bridges: C:E.334 AHY.40: 17 residues within 4Å: Chain D: K.250, D.255, K.262, M.270, D.273, D.332, E.334, T.359, L.360, G.362, D.365, A.451 Chain F: R.425 Ligands: ALA-MLE-TYR-TYR.31, ALA-MLE-TYR-TYR.31, ZN.38, ZN.39 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:D.365 Hydrogen bonds: D:K.262, D:T.359 Water bridges: D:E.334 AHY.50: 17 residues within 4Å: Chain C: R.425 Chain E: K.250, D.255, K.262, M.270, D.273, D.332, E.334, T.359, L.360, G.362, D.365, A.451 Ligands: ALA-MLE-TYR-TYR.41, ALA-MLE-TYR-TYR.41, ZN.48, ZN.49 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:D.365 Hydrogen bonds: E:K.262, E:T.359 Water bridges: E:E.334 AHY.60: 17 residues within 4Å: Chain D: R.425 Chain F: K.250, D.255, K.262, M.270, D.273, D.332, E.334, T.359, L.360, G.362, D.365, A.451 Ligands: ALA-MLE-TYR-TYR.51, ALA-MLE-TYR-TYR.51, ZN.58, ZN.59 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:D.365 Hydrogen bonds: F:K.262, F:T.359 Water bridges: F:E.334

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kraft, M. et al., Binding Structure of the Leucine Aminopeptidase Inhibitor Microginin Fr1. FEBS Lett. (2006)

Release Date

2006-12-06

Peptides

CYTOSOL AMINOPEPTIDASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

CYTOSOL AMINOPEPTIDASE