SMTL ID : 4hxe.1

Pyrococcus horikoshii acylaminoacyl peptidase (uncomplexed)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

homo-hexamer

Ligands

18 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: D.244, E.263 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.244, A:E.263, H2O.2, H2O.4, H2O.4, H2O.6 MG.2: 2 residues within 4Å: Chain A: D.424 Ligands: HEZ.5 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.424, H2O.3, H2O.4, H2O.5, H2O.6, H2O.10 MG.3: 3 residues within 4Å: Chain A: K.99, E.162 Chain C: E.42 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:K.99, A:E.162, H2O.3, H2O.10, H2O.10, H2O.10 MG.10: 2 residues within 4Å: Chain B: D.244, E.263 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.244, B:E.263, H2O.17, H2O.19, H2O.20, H2O.21 MG.11: 2 residues within 4Å: Chain B: D.424 Ligands: HEZ.14 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:D.424, H2O.18, H2O.20, H2O.20, H2O.21, H2O.25 MG.12: 3 residues within 4Å: Chain A: E.42 Chain B: K.99, E.162 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:K.99, B:E.162, H2O.19, H2O.25, H2O.25, H2O.25 MG.19: 2 residues within 4Å: Chain C: D.244, E.263 6 PLIP interactions: 2 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.244, C:E.263, H2O.32, H2O.34, H2O.35, H2O.36 MG.20: 2 residues within 4Å: Chain C: D.424 Ligands: HEZ.23 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:D.424, H2O.33, H2O.35, H2O.35, H2O.36, H2O.40 MG.21: 3 residues within 4Å: Chain B: E.42 Chain C: K.99, E.162 6 PLIP interactions: 2 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:K.99, C:E.162, H2O.34, H2O.40, H2O.40, H2O.40 MG.28: 2 residues within 4Å: Chain D: D.244, E.263 6 PLIP interactions: 2 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.244, D:E.263, H2O.47, H2O.49, H2O.50, H2O.51 MG.29: 2 residues within 4Å: Chain D: D.424 Ligands: HEZ.32 6 PLIP interactions: 1 interactions with chain D, 5 Ligand-Water interactions Metal complexes: D:D.424, H2O.48, H2O.50, H2O.50, H2O.51, H2O.55 MG.30: 3 residues within 4Å: Chain D: K.99, E.162 Chain F: E.42 6 PLIP interactions: 2 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:K.99, D:E.162, H2O.49, H2O.55, H2O.55, H2O.55 MG.37: 2 residues within 4Å: Chain E: D.244, E.263 6 PLIP interactions: 2 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:D.244, E:E.263, H2O.63, H2O.65, H2O.65, H2O.66 MG.38: 2 residues within 4Å: Chain E: D.424 Ligands: HEZ.41 6 PLIP interactions: 1 interactions with chain E, 5 Ligand-Water interactions Metal complexes: E:D.424, H2O.63, H2O.65, H2O.66, H2O.67, H2O.70 MG.39: 3 residues within 4Å: Chain D: E.42 Chain E: K.99, E.162 6 PLIP interactions: 2 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:K.99, E:E.162, H2O.64, H2O.70, H2O.70, H2O.70 MG.46: 2 residues within 4Å: Chain F: D.244, E.263 6 PLIP interactions: 2 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:D.244, F:E.263, H2O.78, H2O.80, H2O.80, H2O.82 MG.47: 2 residues within 4Å: Chain F: D.424 Ligands: HEZ.50 6 PLIP interactions: 1 interactions with chain F, 5 Ligand-Water interactions Metal complexes: F:D.424, H2O.79, H2O.80, H2O.81, H2O.82, H2O.86 MG.48: 3 residues within 4Å: Chain E: E.42 Chain F: K.99, E.162 6 PLIP interactions: 2 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:K.99, F:E.162, H2O.79, H2O.86, H2O.86, H2O.86

36 x HEZ: HEXANE-1,6-DIOL(Non-covalent)

HEZ.4: 8 residues within 4Å: Chain A: K.316, T.318, R.321, P.322, E.324, Y.326, Q.334 Ligands: HEZ.7 Ligand excluded by PLIP HEZ.5: 6 residues within 4Å: Chain A: Y.239, D.424, L.427, L.430, E.431 Ligands: MG.2 Ligand excluded by PLIP HEZ.6: 5 residues within 4Å: Chain A: Y.16, Y.41, I.582, R.583, R.589 Ligand excluded by PLIP HEZ.7: 4 residues within 4Å: Chain A: Q.334, L.335, D.337 Ligands: HEZ.4 Ligand excluded by PLIP HEZ.8: 5 residues within 4Å: Chain A: F.482, K.483, K.535, P.537, Y.607 Ligand excluded by PLIP HEZ.9: 11 residues within 4Å: Chain A: G.387, S.466, Y.467, I.491, S.497, S.501, I.503, F.507, D.508, R.548, C.549 Ligand excluded by PLIP HEZ.13: 8 residues within 4Å: Chain B: K.316, T.318, R.321, P.322, E.324, Y.326, Q.334 Ligands: HEZ.16 Ligand excluded by PLIP HEZ.14: 6 residues within 4Å: Chain B: Y.239, D.424, L.427, L.430, E.431 Ligands: MG.11 Ligand excluded by PLIP HEZ.15: 5 residues within 4Å: Chain B: Y.16, Y.41, I.582, R.583, R.589 Ligand excluded by PLIP HEZ.16: 4 residues within 4Å: Chain B: Q.334, L.335, D.337 Ligands: HEZ.13 Ligand excluded by PLIP HEZ.17: 5 residues within 4Å: Chain B: F.482, K.483, K.535, P.537, Y.607 Ligand excluded by PLIP HEZ.18: 11 residues within 4Å: Chain B: G.387, S.466, Y.467, I.491, S.497, S.501, I.503, F.507, D.508, R.548, C.549 Ligand excluded by PLIP HEZ.22: 8 residues within 4Å: Chain C: K.316, T.318, R.321, P.322, E.324, Y.326, Q.334 Ligands: HEZ.25 Ligand excluded by PLIP HEZ.23: 6 residues within 4Å: Chain C: Y.239, D.424, L.427, L.430, E.431 Ligands: MG.20 Ligand excluded by PLIP HEZ.24: 5 residues within 4Å: Chain C: Y.16, Y.41, I.582, R.583, R.589 Ligand excluded by PLIP HEZ.25: 4 residues within 4Å: Chain C: Q.334, L.335, D.337 Ligands: HEZ.22 Ligand excluded by PLIP HEZ.26: 5 residues within 4Å: Chain C: F.482, K.483, K.535, P.537, Y.607 Ligand excluded by PLIP HEZ.27: 11 residues within 4Å: Chain C: G.387, S.466, Y.467, I.491, S.497, S.501, I.503, F.507, D.508, R.548, C.549 Ligand excluded by PLIP HEZ.31: 8 residues within 4Å: Chain D: K.316, T.318, R.321, P.322, E.324, Y.326, Q.334 Ligands: HEZ.34 Ligand excluded by PLIP HEZ.32: 6 residues within 4Å: Chain D: Y.239, D.424, L.427, L.430, E.431 Ligands: MG.29 Ligand excluded by PLIP HEZ.33: 5 residues within 4Å: Chain D: Y.16, Y.41, I.582, R.583, R.589 Ligand excluded by PLIP HEZ.34: 4 residues within 4Å: Chain D: Q.334, L.335, D.337 Ligands: HEZ.31 Ligand excluded by PLIP HEZ.35: 5 residues within 4Å: Chain D: F.482, K.483, K.535, P.537, Y.607 Ligand excluded by PLIP HEZ.36: 11 residues within 4Å: Chain D: G.387, S.466, Y.467, I.491, S.497, S.501, I.503, F.507, D.508, R.548, C.549 Ligand excluded by PLIP HEZ.40: 8 residues within 4Å: Chain E: K.316, T.318, R.321, P.322, E.324, Y.326, Q.334 Ligands: HEZ.43 Ligand excluded by PLIP HEZ.41: 6 residues within 4Å: Chain E: Y.239, D.424, L.427, L.430, E.431 Ligands: MG.38 Ligand excluded by PLIP HEZ.42: 5 residues within 4Å: Chain E: Y.16, Y.41, I.582, R.583, R.589 Ligand excluded by PLIP HEZ.43: 4 residues within 4Å: Chain E: Q.334, L.335, D.337 Ligands: HEZ.40 Ligand excluded by PLIP HEZ.44: 5 residues within 4Å: Chain E: F.482, K.483, K.535, P.537, Y.607 Ligand excluded by PLIP HEZ.45: 11 residues within 4Å: Chain E: G.387, S.466, Y.467, I.491, S.497, S.501, I.503, F.507, D.508, R.548, C.549 Ligand excluded by PLIP HEZ.49: 8 residues within 4Å: Chain F: K.316, T.318, R.321, P.322, E.324, Y.326, Q.334 Ligands: HEZ.52 Ligand excluded by PLIP HEZ.50: 6 residues within 4Å: Chain F: Y.239, D.424, L.427, L.430, E.431 Ligands: MG.47 Ligand excluded by PLIP HEZ.51: 5 residues within 4Å: Chain F: Y.16, Y.41, I.582, R.583, R.589 Ligand excluded by PLIP HEZ.52: 4 residues within 4Å: Chain F: Q.334, L.335, D.337 Ligands: HEZ.49 Ligand excluded by PLIP HEZ.53: 5 residues within 4Å: Chain F: F.482, K.483, K.535, P.537, Y.607 Ligand excluded by PLIP HEZ.54: 11 residues within 4Å: Chain F: G.387, S.466, Y.467, I.491, S.497, S.501, I.503, F.507, D.508, R.548, C.549 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Menyhard, D.K. et al., A Self-compartmentalizing Hexamer Serine Protease from Pyrococcus Horikoshii: SUBSTRATE SELECTION ACHIEVED THROUGH MULTIMERIZATION. J.Biol.Chem. (2013)

Release Date

2013-05-08

Peptides

Putative uncharacterized protein PH0594: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

D
B

E
B

F
B

Putative uncharacterized protein PH0594

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