SMTL ID : 6f2h.1 (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

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

homo-hexamer

Ligands

4 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 B: Y.120 Ligands: IOD.2 12 PLIP interactions: 11 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:F.35, A:E.36, A:E.36, A:I.40, A:R.75, A:R.75 Hydrogen bonds: 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.3: 10 residues within 4Å: Chain A: Y.120 Chain B: A.8, N.9, S.34, F.35, E.36, I.40, R.75, L.78 Ligands: IOD.4 10 PLIP interactions: 10 interactions with chain B, Hydrophobic interactions: B:F.35, B:E.36, B:E.36, B:R.75, B:R.75 Hydrogen bonds: B:N.9 Salt bridges: B:E.36, B:R.75, B:R.75 pi-Cation interactions: B:F.35 7MT.10: 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.11 12 PLIP interactions: 11 interactions with chain E, 1 Ligand-Ligand interactions Hydrophobic interactions: E:F.35, E:E.36, 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-Cation interactions: E:F.35 Metal complexes: 7MT.10 7MT.14: 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: IOD.15 10 PLIP interactions: 9 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 Salt bridges: F:R.75, F:R.75 pi-Cation interactions: F:F.35 Metal complexes: 7MT.14

5 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: 7MT.3 Ligand excluded by PLIP IOD.6: 3 residues within 4Å: Chain C: N.9, R.75 Ligands: TB.5 Ligand excluded by PLIP IOD.11: 3 residues within 4Å: Chain E: N.9, R.75 Ligands: 7MT.10 Ligand excluded by PLIP IOD.15: 3 residues within 4Å: Chain F: N.9, R.75 Ligands: 7MT.14 Ligand excluded by PLIP

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

TB.5: 2 residues within 4Å: Chain C: R.75 Ligands: IOD.6 No protein-ligand interaction detected (PLIP) TB.7: 1 residues within 4Å: Chain D: R.75 No protein-ligand interaction detected (PLIP) TB.8: 1 residues within 4Å: Chain E: E.160 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.160, E:E.160, H2O.13 TB.9: 2 residues within 4Å: Chain E: K.116, E.133 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.133 TB.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) TB.13: 2 residues within 4Å: Chain F: E.29, Y.31 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.29, F:E.29, H2O.17

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
D

E
E

F
F

Deglycase PH1704

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