SMTL ID : 6f2f.1

Crystal structure of Protease 1 from Pyrococcus Horikoshii co-cystallized in presence of 10 mM Tb-Xo4 and ammonium sulfate.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-hexamer

Ligands

6 x 7MT: Tb-Xo4(Non-covalent)

7MT.1: 11 residues within 4Å: Chain A: A.8, N.9, S.34, F.35, E.36, I.40, V.50, R.75, L.78 Chain D: Y.120 Ligands: SO4.2 13 PLIP interactions: 12 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:F.35, A:F.35, A:E.36, A:I.40, A:R.75, A:R.75 Hydrogen bonds: A:N.9, A:N.9 Salt bridges: A:E.36, A:R.75, A:R.75 pi-Cation interactions: A:F.35 Metal complexes: 7MT.1 7MT.5: 10 residues within 4Å: Chain B: A.8, N.9, S.34, F.35, E.36, I.40, V.50, R.75, L.78 Ligands: SO4.8 13 PLIP interactions: 12 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:F.35, B:F.35, B:E.36, B:I.40, B:R.75, B:R.75 Hydrogen bonds: B:N.9, B:N.9 Salt bridges: B:E.36, B:R.75, B:R.75 pi-Cation interactions: B:F.35 Metal complexes: 7MT.5 7MT.9: 10 residues within 4Å: Chain C: A.8, N.9, S.34, F.35, E.36, I.40, V.50, R.75, L.78 Ligands: SO4.12 12 PLIP interactions: 11 interactions with chain C, 1 Ligand-Ligand interactions Hydrophobic interactions: C:F.35, C:E.36, C:I.40, C:R.75, C:R.75 Hydrogen bonds: C:N.9, C:N.9 Salt bridges: C:E.36, C:R.75, C:R.75 pi-Cation interactions: C:F.35 Metal complexes: 7MT.9 7MT.14: 11 residues within 4Å: Chain A: Y.120 Chain D: A.8, N.9, S.34, F.35, E.36, I.40, V.50, R.75, L.78 Ligands: SO4.15 13 PLIP interactions: 12 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:F.35, D:F.35, D:E.36, D:I.40, D:R.75, D:R.75 Hydrogen bonds: D:N.9, D:N.9 Salt bridges: D:E.36, D:R.75, D:R.75 pi-Cation interactions: D:F.35 Metal complexes: 7MT.14 7MT.18: 10 residues within 4Å: Chain E: A.8, N.9, S.34, F.35, E.36, I.40, V.50, R.75, L.78 Ligands: SO4.21 13 PLIP interactions: 12 interactions with chain E, 1 Ligand-Ligand interactions Hydrophobic interactions: E:F.35, E:F.35, E:E.36, E:I.40, E:R.75, E:R.75 Hydrogen bonds: E:N.9, E:N.9 Salt bridges: E:E.36, E:R.75, E:R.75 pi-Cation interactions: E:F.35 Metal complexes: 7MT.18 7MT.22: 10 residues within 4Å: Chain F: A.8, N.9, S.34, F.35, E.36, I.40, V.50, R.75, L.78 Ligands: SO4.25 12 PLIP interactions: 11 interactions with chain F, 1 Ligand-Ligand interactions Hydrophobic interactions: F:F.35, F:E.36, F:I.40, F:R.75, F:R.75 Hydrogen bonds: F:N.9, F:N.9 Salt bridges: F:E.36, F:R.75, F:R.75 pi-Cation interactions: F:F.35 Metal complexes: 7MT.22

16 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 3 residues within 4Å: Chain A: N.9, R.75 Ligands: 7MT.1 Ligand excluded by PLIP SO4.3: 2 residues within 4Å: Chain A: E.138, R.149 Ligand excluded by PLIP SO4.6: 2 residues within 4Å: Chain B: E.138, R.149 Ligand excluded by PLIP SO4.7: 5 residues within 4Å: Chain B: K.2, Y.31, L.52, E.61, F.62 Ligand excluded by PLIP SO4.8: 3 residues within 4Å: Chain B: N.9, R.75 Ligands: 7MT.5 Ligand excluded by PLIP SO4.10: 2 residues within 4Å: Chain C: E.138, R.149 Ligand excluded by PLIP SO4.11: 5 residues within 4Å: Chain B: K.43, R.71 Chain C: E.10, R.71, R.75 Ligand excluded by PLIP SO4.12: 3 residues within 4Å: Chain C: N.9, R.75 Ligands: 7MT.9 Ligand excluded by PLIP SO4.15: 3 residues within 4Å: Chain D: N.9, R.75 Ligands: 7MT.14 Ligand excluded by PLIP SO4.16: 2 residues within 4Å: Chain D: E.138, R.149 Ligand excluded by PLIP SO4.19: 2 residues within 4Å: Chain E: E.138, R.149 Ligand excluded by PLIP SO4.20: 5 residues within 4Å: Chain E: K.2, Y.31, L.52, E.61, F.62 Ligand excluded by PLIP SO4.21: 3 residues within 4Å: Chain E: N.9, R.75 Ligands: 7MT.18 Ligand excluded by PLIP SO4.23: 2 residues within 4Å: Chain F: E.138, R.149 Ligand excluded by PLIP SO4.24: 5 residues within 4Å: Chain E: K.43, R.71 Chain F: E.10, R.71, R.75 Ligand excluded by PLIP SO4.25: 3 residues within 4Å: Chain F: N.9, R.75 Ligands: 7MT.22 Ligand excluded by PLIP

2 x TB: TERBIUM(III) ION(Non-functional Binders)

TB.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) TB.17: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x 2HA: Dihydroxyacetone(Non-covalent)

2HA.13: 6 residues within 4Å: Chain C: G.114, I.128, G.131, V.132, E.133, W.134 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.131 Water bridges: C:E.133 2HA.26: 6 residues within 4Å: Chain F: G.114, I.128, G.131, V.132, E.133, W.134 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:G.131 Water bridges: F:E.133

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Engilberge, S. et al., Unveiling the Binding Modes of the Crystallophore, a Terbium-based Nucleating and Phasing Molecular Agent for Protein Crystallography. Chemistry (2018)

Release Date

2018-10-03

Peptides

Deglycase PH1704: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
A

E
B

F
C

Deglycase PH1704

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