SMTL ID : 3ajv.1

Splicing endonuclease from Aeropyrum pernix

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-2-2-mer

Ligands

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: S.102, L.103, D.104, S.143, Y.146 Chain D: G.16, D.17 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain D Hydrogen bonds: A:L.103, A:D.104, A:S.143, A:Y.146, A:Y.146 Water bridges: D:R.55, D:R.55, D:R.55, D:R.55 GOL.2: 4 residues within 4Å: Chain A: D.111, K.115, I.178, Y.180 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.115, A:K.115 Water bridges: A:I.178, A:Y.180, B:F.184 GOL.3: 6 residues within 4Å: Chain B: R.126, A.134, P.135, F.136, R.163, K.165 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.134, B:P.135 Water bridges: B:R.126, B:I.137 GOL.4: 6 residues within 4Å: Chain B: V.150, E.151, R.154 Chain D: R.94, G.119, D.121 9 PLIP interactions: 2 interactions with chain B, 7 interactions with chain D Hydrogen bonds: B:R.154, D:R.94, D:R.154 Water bridges: B:V.150, D:G.119, D:D.121, D:D.121, D:D.121, D:A.140 GOL.5: 5 residues within 4Å: Chain B: Y.31, E.43, K.44, R.113, P.129 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:R.113, B:P.129 Water bridges: B:Y.31, B:Q.38, B:Q.38, B:K.117 GOL.6: 8 residues within 4Å: Chain B: Q.38, P.39, L.40, E.43 Chain C: R.114, G.176, L.177, I.178 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:G.176, C:I.178, B:Q.38, B:V.42 GOL.8: 6 residues within 4Å: Chain B: G.16, D.17 Chain C: S.102, L.103, D.104, S.143 7 PLIP interactions: 3 interactions with chain C, 4 interactions with chain B Hydrogen bonds: C:L.103, C:D.104, C:S.143, B:D.17 Water bridges: B:D.17, B:D.17, B:R.55 GOL.9: 4 residues within 4Å: Chain D: A.134, P.135, F.136, R.163 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:A.134, D:K.165 Water bridges: D:A.134, D:I.137 GOL.10: 6 residues within 4Å: Chain B: R.94, G.119, D.121 Chain D: V.150, E.151, R.154 7 PLIP interactions: 3 interactions with chain D, 4 interactions with chain B Hydrogen bonds: D:V.150, B:R.94, B:R.94, B:D.121 Water bridges: D:R.154, D:R.154, B:D.121 GOL.11: 6 residues within 4Å: Chain D: Y.31, Y.35, P.45, G.47, P.129, G.130 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:P.45

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

CL.7: 4 residues within 4Å: Chain B: S.57, I.59, E.60 Chain C: R.174 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: R.174 Chain D: S.57, I.59, E.60 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Okuda, M. et al., A Conserved Lysine Residue in the Crenarchaea-Specific Loop is Important for the Crenarchaeal Splicing Endonuclease Activity. J.Mol.Biol. (2011)

Release Date

2010-11-17

Peptides

Putative uncharacterized protein: AC
tRNA-splicing endonuclease: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

B
B

D
D

Putative uncharacterized protein

tRNA-splicing endonuclease