SMTL ID : 4hxg.1 (1 other biounit)

Pyrococcus horikoshii acylaminoacyl peptidase (orthorhombic crystal form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-hexamer

Ligands

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

HEZ.1: 10 residues within 4Å: Chain A: G.387, A.466, Y.467, I.491, S.497, S.501, F.507, D.508, R.548, C.549 Ligand excluded by PLIP HEZ.2: 5 residues within 4Å: Chain A: Y.395, K.397, I.465, G.579, I.582 Ligand excluded by PLIP HEZ.3: 4 residues within 4Å: Chain A: A.265, Q.266, W.302, M.304 Ligand excluded by PLIP HEZ.6: 9 residues within 4Å: Chain B: G.386, G.387, A.466, Y.467, I.491, S.497, S.501, D.508, R.548 Ligand excluded by PLIP HEZ.7: 9 residues within 4Å: Chain B: W.140, L.544, D.546, P.550, L.551 Chain E: L.544, D.546, P.550, L.551 Ligand excluded by PLIP HEZ.9: 10 residues within 4Å: Chain C: G.386, G.387, A.466, Y.467, S.497, S.501, I.503, F.507, D.508, R.548 Ligand excluded by PLIP HEZ.12: 12 residues within 4Å: Chain D: G.387, A.466, Y.467, I.491, S.497, S.501, F.507, D.508, R.548, C.549, H.578 Ligands: HEZ.18 Ligand excluded by PLIP HEZ.13: 8 residues within 4Å: Chain A: W.140, L.544, D.546, P.550, L.551 Chain D: L.544, D.546, L.551 Ligand excluded by PLIP HEZ.14: 5 residues within 4Å: Chain D: Y.239, D.424, L.427, R.428, L.430 Ligand excluded by PLIP HEZ.15: 4 residues within 4Å: Chain D: Y.16, Y.41, R.583, R.589 Ligand excluded by PLIP HEZ.16: 5 residues within 4Å: Chain D: F.482, K.483, K.535, P.537, Y.607 Ligand excluded by PLIP HEZ.17: 6 residues within 4Å: Chain D: Y.220, I.222, Y.232, A.265, Q.266, A.267 Ligand excluded by PLIP HEZ.18: 7 residues within 4Å: Chain D: G.386, I.465, A.466, H.578, S.581, I.582 Ligands: HEZ.12 Ligand excluded by PLIP HEZ.19: 8 residues within 4Å: Chain D: V.240, S.241, G.387, P.388, K.389, V.429, F.507, V.511 Ligand excluded by PLIP HEZ.23: 11 residues within 4Å: Chain E: G.386, G.387, A.466, Y.467, I.491, S.497, S.501, F.507, D.508, R.548, C.549 Ligand excluded by PLIP HEZ.24: 7 residues within 4Å: Chain E: K.316, E.317, R.321, P.322, E.324, Y.326, Q.334 Ligand excluded by PLIP HEZ.25: 4 residues within 4Å: Chain E: Y.16, Y.41, I.582, R.589 Ligand excluded by PLIP HEZ.29: 10 residues within 4Å: Chain F: G.387, A.466, Y.467, I.491, S.497, S.501, I.503, F.507, D.508, R.548 Ligand excluded by PLIP HEZ.30: 8 residues within 4Å: Chain C: L.544, L.551 Chain F: S.543, L.544, D.546, Y.547, P.550, L.551 Ligand excluded by PLIP HEZ.31: 6 residues within 4Å: Chain F: Y.220, I.222, Y.232, A.265, Q.266, A.267 Ligand excluded by PLIP

13 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: K.99, E.162 Chain C: E.42 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:K.99, A:E.162, H2O.6, H2O.11, H2O.12 MG.5: 2 residues within 4Å: Chain A: D.244, E.263 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.244, A:E.263, H2O.1, H2O.6 MG.8: 3 residues within 4Å: Chain A: E.42 Chain B: K.99, E.162 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:K.99, B:E.162, H2O.3, H2O.7 MG.10: 3 residues within 4Å: Chain B: E.42 Chain C: K.99, E.162 5 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: C:K.99, C:E.162, B:E.42, H2O.7, H2O.10 MG.11: 2 residues within 4Å: Chain C: D.244, E.263 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.244, C:E.263, H2O.10, H2O.10, H2O.12 MG.20: 2 residues within 4Å: Chain D: D.244, E.263 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.244, D:E.263, H2O.12, H2O.17, H2O.17 MG.21: 4 residues within 4Å: Chain D: K.99, E.162 Chain E: E.42, T.44 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.162, H2O.20, H2O.21, H2O.24 MG.26: 3 residues within 4Å: Chain E: Y.232, D.244, E.263 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.244, E:E.263, E:E.263, H2O.20, H2O.27 MG.27: 3 residues within 4Å: Chain E: K.99, E.162 Chain F: E.42 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:K.99, H2O.25, H2O.30, H2O.30, H2O.30 MG.28: 2 residues within 4Å: Chain D: E.163 Chain E: E.37 No protein-ligand interaction detected (PLIP) MG.32: 2 residues within 4Å: Chain F: D.244, E.263 5 PLIP interactions: 2 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.244, F:E.263, H2O.28, H2O.30, H2O.33 MG.33: 3 residues within 4Å: Chain D: E.42 Chain F: K.99, E.162 5 PLIP interactions: 2 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:K.99, F:E.162, H2O.14, H2O.17, H2O.31 MG.34: 2 residues within 4Å: Chain E: E.163 Chain F: E.37 No protein-ligand interaction detected (PLIP)

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

CL.22: 4 residues within 4Å: Chain D: R.55 Chain F: K.98, T.159, E.160 Ligand excluded by PLIP CL.35: 3 residues within 4Å: Chain E: K.98, E.160 Chain F: R.55 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
A

B
B

C
C

D
D

E
E

F
F

Putative uncharacterized protein PH0594

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