SMTL ID : 4hxf.1

Acylaminoacyl peptidase in complex with Z-Gly-Gly-Phe-chloromethyl ketone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-hexamer

Ligands

6 x Y3A: N-[(benzyloxy)carbonyl]glycyl-N-[(2S,3R)-4-chloro-3-hydroxy-1-phenylbutan-2-yl]glycinamide(Covalent)

Y3A.1: 14 residues within 4Å: Chain A: G.386, G.387, S.466, Y.467, I.491, W.494, S.497, F.507, D.508, R.548, C.549, H.578 Ligands: HEZ.10, HEZ.15 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:I.491, A:W.494, A:F.507 Hydrogen bonds: A:G.387, A:G.387, A:G.387, A:Y.467, A:R.548 Y3A.18: 14 residues within 4Å: Chain B: G.386, G.387, S.466, Y.467, I.491, W.494, S.497, F.507, D.508, R.548, C.549, H.578 Ligands: HEZ.27, HEZ.32 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.491, B:W.494, B:F.507 Hydrogen bonds: B:G.387, B:G.387, B:G.387, B:Y.467, B:R.548 Y3A.35: 14 residues within 4Å: Chain C: G.386, G.387, S.466, Y.467, I.491, W.494, S.497, F.507, D.508, R.548, C.549, H.578 Ligands: HEZ.44, HEZ.49 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:I.491, C:W.494, C:F.507 Hydrogen bonds: C:G.387, C:G.387, C:G.387, C:Y.467, C:R.548 Y3A.52: 14 residues within 4Å: Chain D: G.386, G.387, S.466, Y.467, I.491, W.494, S.497, F.507, D.508, R.548, C.549, H.578 Ligands: HEZ.61, HEZ.66 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:I.491, D:W.494, D:F.507 Hydrogen bonds: D:G.387, D:G.387, D:G.387, D:Y.467, D:R.548 Y3A.69: 14 residues within 4Å: Chain E: G.386, G.387, S.466, Y.467, I.491, W.494, S.497, F.507, D.508, R.548, C.549, H.578 Ligands: HEZ.78, HEZ.83 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:I.491, E:W.494, E:F.507 Hydrogen bonds: E:G.387, E:G.387, E:G.387, E:Y.467, E:R.548 Y3A.86: 14 residues within 4Å: Chain F: G.386, G.387, S.466, Y.467, I.491, W.494, S.497, F.507, D.508, R.548, C.549, H.578 Ligands: HEZ.95, HEZ.100 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:I.491, F:W.494, F:F.507 Hydrogen bonds: F:G.387, F:G.387, F:G.387, F:Y.467, F:R.548

30 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.424 Ligands: HEZ.7 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.424, H2O.4, H2O.7 MG.3: 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.3, H2O.3, H2O.7, H2O.7 MG.4: 1 residues within 4Å: Chain B: E.163 No protein-ligand interaction detected (PLIP) MG.5: 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.53, H2O.58, H2O.58 MG.6: 1 residues within 4Å: Chain A: E.127 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:E.127, H2O.5, H2O.12, H2O.13, H2O.19, H2O.22 MG.19: 2 residues within 4Å: Chain B: D.424 Ligands: HEZ.24 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.424, H2O.29, H2O.33 MG.20: 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.28, H2O.28, H2O.32, H2O.33 MG.21: 1 residues within 4Å: Chain C: E.163 No protein-ligand interaction detected (PLIP) MG.22: 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.2, H2O.7, H2O.7, H2O.29 MG.23: 1 residues within 4Å: Chain B: E.127 6 PLIP interactions: 1 interactions with chain B, 5 Ligand-Water interactions Metal complexes: B:E.127, H2O.31, H2O.37, H2O.39, H2O.44, H2O.47 MG.36: 2 residues within 4Å: Chain C: D.424 Ligands: HEZ.41 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.424, H2O.54, H2O.58 MG.37: 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.53, H2O.53, H2O.58, H2O.58 MG.38: 1 residues within 4Å: Chain A: E.163 No protein-ligand interaction detected (PLIP) MG.39: 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.28, H2O.32, H2O.32, H2O.54 MG.40: 1 residues within 4Å: Chain C: E.127 6 PLIP interactions: 1 interactions with chain C, 5 Ligand-Water interactions Metal complexes: C:E.127, H2O.56, H2O.63, H2O.64, H2O.69, H2O.72 MG.53: 2 residues within 4Å: Chain D: D.424 Ligands: HEZ.58 3 PLIP interactions: 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.424, H2O.80, H2O.83 MG.54: 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.78, H2O.79, H2O.83, H2O.83 MG.55: 1 residues within 4Å: Chain E: E.163 No protein-ligand interaction detected (PLIP) MG.56: 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.79, H2O.128, H2O.133, H2O.133 MG.57: 1 residues within 4Å: Chain D: E.127 6 PLIP interactions: 1 interactions with chain D, 5 Ligand-Water interactions Metal complexes: D:E.127, H2O.81, H2O.88, H2O.89, H2O.94, H2O.97 MG.70: 2 residues within 4Å: Chain E: D.424 Ligands: HEZ.75 3 PLIP interactions: 1 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.424, H2O.105, H2O.108 MG.71: 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.104, H2O.104, H2O.108, H2O.108 MG.72: 1 residues within 4Å: Chain F: E.163 No protein-ligand interaction detected (PLIP) MG.73: 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.78, H2O.83, H2O.83, H2O.104 MG.74: 1 residues within 4Å: Chain E: E.127 6 PLIP interactions: 1 interactions with chain E, 5 Ligand-Water interactions Metal complexes: E:E.127, H2O.106, H2O.113, H2O.114, H2O.119, H2O.122 MG.87: 2 residues within 4Å: Chain F: D.424 Ligands: HEZ.92 3 PLIP interactions: 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.424, H2O.130, H2O.133 MG.88: 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.129, H2O.129, H2O.133, H2O.133 MG.89: 1 residues within 4Å: Chain D: E.163 No protein-ligand interaction detected (PLIP) MG.90: 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.103, H2O.108, H2O.108, H2O.129 MG.91: 1 residues within 4Å: Chain F: E.127 6 PLIP interactions: 1 interactions with chain F, 5 Ligand-Water interactions Metal complexes: F:E.127, H2O.131, H2O.138, H2O.139, H2O.145, H2O.148

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

HEZ.7: 7 residues within 4Å: Chain A: Y.239, D.424, L.427, L.430, E.431 Ligands: MG.2, HEZ.8 Ligand excluded by PLIP HEZ.8: 4 residues within 4Å: Chain A: E.431, R.432, N.521 Ligands: HEZ.7 Ligand excluded by PLIP HEZ.9: 6 residues within 4Å: Chain A: Y.220, I.222, Y.232, A.265, Q.266, A.267 Ligand excluded by PLIP HEZ.10: 7 residues within 4Å: Chain A: Y.395, K.397, I.465, H.578, G.579, S.581 Ligands: Y3A.1 Ligand excluded by PLIP HEZ.11: 6 residues within 4Å: Chain A: D.480, F.482, K.483, K.535, A.536, P.537 Ligand excluded by PLIP HEZ.12: 11 residues within 4Å: Chain A: W.140, H.542, S.543, L.544, D.546, Y.547, P.550, L.551 Chain D: W.140, L.544 Ligands: HEZ.63 Ligand excluded by PLIP HEZ.13: 5 residues within 4Å: Chain A: R.523, F.529, Y.530, K.532 Chain D: E.518 Ligand excluded by PLIP HEZ.14: 6 residues within 4Å: Chain A: E.350, R.352, Y.367, I.368, K.369, E.452 Ligand excluded by PLIP HEZ.15: 7 residues within 4Å: Chain A: F.197, V.240, S.241, K.389, F.507, R.548 Ligands: Y3A.1 Ligand excluded by PLIP HEZ.16: 6 residues within 4Å: Chain A: I.260, L.278, E.280, Y.287, V.293, E.295 Ligand excluded by PLIP HEZ.24: 7 residues within 4Å: Chain B: Y.239, D.424, L.427, L.430, E.431 Ligands: MG.19, HEZ.25 Ligand excluded by PLIP HEZ.25: 4 residues within 4Å: Chain B: E.431, R.432, N.521 Ligands: HEZ.24 Ligand excluded by PLIP HEZ.26: 6 residues within 4Å: Chain B: Y.220, I.222, Y.232, A.265, Q.266, A.267 Ligand excluded by PLIP HEZ.27: 7 residues within 4Å: Chain B: Y.395, K.397, I.465, H.578, G.579, S.581 Ligands: Y3A.18 Ligand excluded by PLIP HEZ.28: 6 residues within 4Å: Chain B: D.480, F.482, K.483, K.535, A.536, P.537 Ligand excluded by PLIP HEZ.29: 11 residues within 4Å: Chain B: W.140, H.542, S.543, L.544, D.546, Y.547, P.550, L.551 Chain F: W.140, L.544 Ligands: HEZ.97 Ligand excluded by PLIP HEZ.30: 5 residues within 4Å: Chain B: R.523, F.529, Y.530, K.532 Chain F: E.518 Ligand excluded by PLIP HEZ.31: 6 residues within 4Å: Chain B: E.350, R.352, Y.367, I.368, K.369, E.452 Ligand excluded by PLIP HEZ.32: 7 residues within 4Å: Chain B: F.197, V.240, S.241, K.389, F.507, R.548 Ligands: Y3A.18 Ligand excluded by PLIP HEZ.33: 6 residues within 4Å: Chain B: I.260, L.278, E.280, Y.287, V.293, E.295 Ligand excluded by PLIP HEZ.41: 7 residues within 4Å: Chain C: Y.239, D.424, L.427, L.430, E.431 Ligands: MG.36, HEZ.42 Ligand excluded by PLIP HEZ.42: 4 residues within 4Å: Chain C: E.431, R.432, N.521 Ligands: HEZ.41 Ligand excluded by PLIP HEZ.43: 6 residues within 4Å: Chain C: Y.220, I.222, Y.232, A.265, Q.266, A.267 Ligand excluded by PLIP HEZ.44: 7 residues within 4Å: Chain C: Y.395, K.397, I.465, H.578, G.579, S.581 Ligands: Y3A.35 Ligand excluded by PLIP HEZ.45: 6 residues within 4Å: Chain C: D.480, F.482, K.483, K.535, A.536, P.537 Ligand excluded by PLIP HEZ.46: 11 residues within 4Å: Chain C: W.140, H.542, S.543, L.544, D.546, Y.547, P.550, L.551 Chain E: W.140, L.544 Ligands: HEZ.80 Ligand excluded by PLIP HEZ.47: 5 residues within 4Å: Chain C: R.523, F.529, Y.530, K.532 Chain E: E.518 Ligand excluded by PLIP HEZ.48: 6 residues within 4Å: Chain C: E.350, R.352, Y.367, I.368, K.369, E.452 Ligand excluded by PLIP HEZ.49: 7 residues within 4Å: Chain C: F.197, V.240, S.241, K.389, F.507, R.548 Ligands: Y3A.35 Ligand excluded by PLIP HEZ.50: 6 residues within 4Å: Chain C: I.260, L.278, E.280, Y.287, V.293, E.295 Ligand excluded by PLIP HEZ.58: 7 residues within 4Å: Chain D: Y.239, D.424, L.427, L.430, E.431 Ligands: MG.53, HEZ.59 Ligand excluded by PLIP HEZ.59: 4 residues within 4Å: Chain D: E.431, R.432, N.521 Ligands: HEZ.58 Ligand excluded by PLIP HEZ.60: 6 residues within 4Å: Chain D: Y.220, I.222, Y.232, A.265, Q.266, A.267 Ligand excluded by PLIP HEZ.61: 7 residues within 4Å: Chain D: Y.395, K.397, I.465, H.578, G.579, S.581 Ligands: Y3A.52 Ligand excluded by PLIP HEZ.62: 6 residues within 4Å: Chain D: D.480, F.482, K.483, K.535, A.536, P.537 Ligand excluded by PLIP HEZ.63: 11 residues within 4Å: Chain A: W.140, L.544 Chain D: W.140, H.542, S.543, L.544, D.546, Y.547, P.550, L.551 Ligands: HEZ.12 Ligand excluded by PLIP HEZ.64: 5 residues within 4Å: Chain A: E.518 Chain D: R.523, F.529, Y.530, K.532 Ligand excluded by PLIP HEZ.65: 6 residues within 4Å: Chain D: E.350, R.352, Y.367, I.368, K.369, E.452 Ligand excluded by PLIP HEZ.66: 7 residues within 4Å: Chain D: F.197, V.240, S.241, K.389, F.507, R.548 Ligands: Y3A.52 Ligand excluded by PLIP HEZ.67: 6 residues within 4Å: Chain D: I.260, L.278, E.280, Y.287, V.293, E.295 Ligand excluded by PLIP HEZ.75: 7 residues within 4Å: Chain E: Y.239, D.424, L.427, L.430, E.431 Ligands: MG.70, HEZ.76 Ligand excluded by PLIP HEZ.76: 4 residues within 4Å: Chain E: E.431, R.432, N.521 Ligands: HEZ.75 Ligand excluded by PLIP HEZ.77: 6 residues within 4Å: Chain E: Y.220, I.222, Y.232, A.265, Q.266, A.267 Ligand excluded by PLIP HEZ.78: 7 residues within 4Å: Chain E: Y.395, K.397, I.465, H.578, G.579, S.581 Ligands: Y3A.69 Ligand excluded by PLIP HEZ.79: 6 residues within 4Å: Chain E: D.480, F.482, K.483, K.535, A.536, P.537 Ligand excluded by PLIP HEZ.80: 11 residues within 4Å: Chain C: W.140, L.544 Chain E: W.140, H.542, S.543, L.544, D.546, Y.547, P.550, L.551 Ligands: HEZ.46 Ligand excluded by PLIP HEZ.81: 5 residues within 4Å: Chain C: E.518 Chain E: R.523, F.529, Y.530, K.532 Ligand excluded by PLIP HEZ.82: 6 residues within 4Å: Chain E: E.350, R.352, Y.367, I.368, K.369, E.452 Ligand excluded by PLIP HEZ.83: 7 residues within 4Å: Chain E: F.197, V.240, S.241, K.389, F.507, R.548 Ligands: Y3A.69 Ligand excluded by PLIP HEZ.84: 6 residues within 4Å: Chain E: I.260, L.278, E.280, Y.287, V.293, E.295 Ligand excluded by PLIP HEZ.92: 7 residues within 4Å: Chain F: Y.239, D.424, L.427, L.430, E.431 Ligands: MG.87, HEZ.93 Ligand excluded by PLIP HEZ.93: 4 residues within 4Å: Chain F: E.431, R.432, N.521 Ligands: HEZ.92 Ligand excluded by PLIP HEZ.94: 6 residues within 4Å: Chain F: Y.220, I.222, Y.232, A.265, Q.266, A.267 Ligand excluded by PLIP HEZ.95: 7 residues within 4Å: Chain F: Y.395, K.397, I.465, H.578, G.579, S.581 Ligands: Y3A.86 Ligand excluded by PLIP HEZ.96: 6 residues within 4Å: Chain F: D.480, F.482, K.483, K.535, A.536, P.537 Ligand excluded by PLIP HEZ.97: 11 residues within 4Å: Chain B: W.140, L.544 Chain F: W.140, H.542, S.543, L.544, D.546, Y.547, P.550, L.551 Ligands: HEZ.29 Ligand excluded by PLIP HEZ.98: 5 residues within 4Å: Chain B: E.518 Chain F: R.523, F.529, Y.530, K.532 Ligand excluded by PLIP HEZ.99: 6 residues within 4Å: Chain F: E.350, R.352, Y.367, I.368, K.369, E.452 Ligand excluded by PLIP HEZ.100: 7 residues within 4Å: Chain F: F.197, V.240, S.241, K.389, F.507, R.548 Ligands: Y3A.86 Ligand excluded by PLIP HEZ.101: 6 residues within 4Å: Chain F: I.260, L.278, E.280, Y.287, V.293, E.295 Ligand excluded by PLIP

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

CL.17: 3 residues within 4Å: Chain A: K.98, E.160 Chain C: R.55 Ligand excluded by PLIP CL.34: 3 residues within 4Å: Chain A: R.55 Chain B: K.98, E.160 Ligand excluded by PLIP CL.51: 3 residues within 4Å: Chain B: R.55 Chain C: K.98, E.160 Ligand excluded by PLIP CL.68: 3 residues within 4Å: Chain D: K.98, E.160 Chain F: R.55 Ligand excluded by PLIP CL.85: 3 residues within 4Å: Chain D: R.55 Chain E: K.98, E.160 Ligand excluded by PLIP CL.102: 3 residues within 4Å: Chain E: R.55 Chain F: K.98, E.160 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

Related Entries With Identical Sequence