SMTL ID : 6hf6.1

Crystal structure of the Protease 1 (E29A,E60A,E80A) from Pyrococcus horikoshii co-crystallized with Tb-Xo4.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 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: MLI.2 12 PLIP interactions: 12 interactions with chain A, 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 7MT.5: 11 residues within 4Å: Chain B: A.8, N.9, S.34, F.35, E.36, I.40, V.50, R.75, L.78 Chain C: Y.120 Ligands: MLI.6 13 PLIP interactions: 13 interactions with chain B, 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 Water bridges: B:R.75 Salt bridges: B:E.36, B:R.75, B:R.75 pi-Cation interactions: B:F.35 7MT.8: 11 residues within 4Å: Chain B: Y.120 Chain C: A.8, N.9, S.34, F.35, E.36, I.40, V.50, R.75, L.78 Ligands: MLI.9 10 PLIP interactions: 10 interactions with chain C, Hydrophobic interactions: 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 7MT.11: 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: MLI.12 12 PLIP interactions: 12 interactions with chain D, 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 7MT.15: 11 residues within 4Å: Chain E: A.8, N.9, S.34, F.35, E.36, I.40, V.50, R.75, L.78 Chain F: Y.120 Ligands: MLI.16 13 PLIP interactions: 13 interactions with chain E, 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 Water bridges: E:R.75 Salt bridges: E:E.36, E:R.75, E:R.75 pi-Cation interactions: E:F.35 7MT.18: 11 residues within 4Å: Chain E: Y.120 Chain F: A.8, N.9, S.34, F.35, E.36, I.40, V.50, R.75, L.78 Ligands: MLI.19 10 PLIP interactions: 10 interactions with chain F, Hydrophobic interactions: 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

6 x MLI: MALONATE ION(Non-functional Binders)

MLI.2: 3 residues within 4Å: Chain A: N.9, R.75 Ligands: 7MT.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.9 Salt bridges: A:R.75, A:R.75 MLI.6: 4 residues within 4Å: Chain B: N.9, E.10, R.75 Ligands: 7MT.5 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.9 Water bridges: B:R.75 Salt bridges: B:R.75, B:R.75 MLI.9: 4 residues within 4Å: Chain C: N.9, E.10, R.75 Ligands: 7MT.8 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.9 Salt bridges: C:R.75, C:R.75 MLI.12: 3 residues within 4Å: Chain D: N.9, R.75 Ligands: 7MT.11 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.9 Salt bridges: D:R.75, D:R.75 MLI.16: 4 residues within 4Å: Chain E: N.9, E.10, R.75 Ligands: 7MT.15 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:N.9 Water bridges: E:R.75 Salt bridges: E:R.75, E:R.75 MLI.19: 4 residues within 4Å: Chain F: N.9, E.10, R.75 Ligands: 7MT.18 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:N.9 Salt bridges: F:R.75, F:R.75

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

TB.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) TB.4: 4 residues within 4Å: Chain A: E.10, R.71, R.75 Chain D: K.43 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.10, H2O.28 TB.7: 3 residues within 4Å: Chain B: E.10, R.71, R.75 No protein-ligand interaction detected (PLIP) TB.10: 4 residues within 4Å: Chain B: R.71 Chain C: E.10, R.71, R.75 No protein-ligand interaction detected (PLIP) TB.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) TB.14: 4 residues within 4Å: Chain A: K.43 Chain D: E.10, R.71, R.75 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.10, H2O.6 TB.17: 3 residues within 4Å: Chain E: E.10, R.71, R.75 No protein-ligand interaction detected (PLIP) TB.20: 4 residues within 4Å: Chain E: R.71 Chain F: E.10, R.71, R.75 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Engilberge, S. et al., Protein crystal structure determination with the crystallophore, a nucleating and phasing agent. J.Appl.Crystallogr. (2019)

Release Date

2019-06-19

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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