SMTL ID : 6f2h.2 (1 other biounit)

Structure of Protease 1 from Pyrococcus horikoshii co-crystallized in presence of 10 mM Tb-Xo4 and potassium iodide.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-hexamer

Ligands

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

7MT.1: 10 residues within 4Å: Chain A: A.8, N.9, S.34, F.35, E.36, I.40, V.50, R.75, L.78 Ligands: IOD.2 12 PLIP interactions: 11 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: 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: 9 residues within 4Å: Chain C: A.8, N.9, S.34, F.35, E.36, I.40, R.75, L.78 Ligands: IOD.6 9 PLIP interactions: 9 interactions with chain C, Hydrophobic interactions: C:F.35, C:E.36, C:E.36, C:R.75 Hydrogen bonds: C:N.9 Salt bridges: C:E.36, C:R.75, C:R.75 pi-Cation interactions: C:F.35 7MT.8: 9 residues within 4Å: Chain D: A.8, N.9, S.34, F.35, E.36, I.40, R.75, L.78 Ligands: IOD.9 13 PLIP interactions: 12 interactions with chain D, 1 Ligand-Ligand interactions Hydrophobic interactions: D:F.35, D:E.36, D:E.36, 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-Stacking: D:F.35 pi-Cation interactions: D:F.35 Metal complexes: 7MT.8 7MT.11: 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: IOD.12 11 PLIP interactions: 10 interactions with chain E, 1 Ligand-Ligand interactions Hydrophobic interactions: E:E.36, E:I.40, E:R.75, E:R.75 Hydrogen bonds: E:N.9 Salt bridges: E:E.36, E:R.75, E:R.75 pi-Stacking: E:F.35 pi-Cation interactions: E:F.35 Metal complexes: 7MT.11 7MT.13: 9 residues within 4Å: Chain F: A.8, N.9, S.34, F.35, E.36, I.40, R.75, L.78 Ligands: IOD.14 12 PLIP interactions: 11 interactions with chain F, 1 Ligand-Ligand interactions Hydrophobic interactions: F:E.36, 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.13

6 x IOD: IODIDE ION(Non-functional Binders)

IOD.2: 3 residues within 4Å: Chain A: N.9, R.75 Ligands: 7MT.1 Ligand excluded by PLIP IOD.4: 3 residues within 4Å: Chain B: N.9, R.75 Ligands: TB.3 Ligand excluded by PLIP IOD.6: 3 residues within 4Å: Chain C: N.9, R.75 Ligands: 7MT.5 Ligand excluded by PLIP IOD.9: 3 residues within 4Å: Chain D: N.9, R.75 Ligands: 7MT.8 Ligand excluded by PLIP IOD.12: 2 residues within 4Å: Chain E: N.9 Ligands: 7MT.11 Ligand excluded by PLIP IOD.14: 3 residues within 4Å: Chain F: N.9, R.75 Ligands: 7MT.13 Ligand excluded by PLIP

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

TB.3: 2 residues within 4Å: Chain B: R.75 Ligands: IOD.4 No protein-ligand interaction detected (PLIP) TB.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) TB.10: 1 residues within 4Å: Chain E: E.60 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:E.60, E:E.60

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
G

B
H

C
I

D
J

E
K

F
L

Deglycase PH1704

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