SMTL ID : 2vug.1

The structure of an archaeal homodimeric RNA ligase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-dimer

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 17 residues within 4Å: Chain A: F.75, H.77, I.78, R.80, E.100, E.101, K.102, V.103, N.107, R.122, E.154, F.179, V.207, I.237, K.239, K.248 Chain B: D.389 17 PLIP interactions: 1 interactions with chain B, 16 interactions with chain A Hydrogen bonds: B:D.389, A:H.77, A:I.78, A:I.78, A:R.80, A:E.100, A:K.102, A:V.103, A:N.107, A:R.122, A:R.122, A:K.239, A:K.248 Salt bridges: A:K.102, A:K.248 pi-Stacking: A:F.179, A:F.179 ANP.4: 17 residues within 4Å: Chain A: D.389 Chain B: F.75, H.77, I.78, R.80, E.100, E.101, K.102, V.103, N.107, R.122, E.154, F.179, V.207, I.237, K.239, K.248 16 PLIP interactions: 15 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.77, B:I.78, B:I.78, B:R.80, B:E.100, B:V.103, B:N.107, B:R.122, B:R.122, B:K.239, B:K.248, A:D.389 Water bridges: B:R.80 Salt bridges: B:K.102, B:K.248 pi-Stacking: B:F.179

5 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 4 residues within 4Å: Chain A: Q.308 Chain B: K.291, G.292, F.295 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.295, A:Q.308 Hydrogen bonds: B:I.290, B:G.292 MPD.3: 4 residues within 4Å: Chain A: V.265, L.269, R.369, Y.371 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.265 Hydrogen bonds: A:E.268 MPD.5: 4 residues within 4Å: Chain B: E.352, I.353, V.354, D.355 No protein-ligand interaction detected (PLIP) MPD.6: 7 residues within 4Å: Chain B: V.164, I.261, V.265, L.269, E.325, R.369, Y.371 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.261, B:V.265, B:Y.371 MPD.7: 6 residues within 4Å: Chain A: S.276, S.279 Chain B: Y.267, E.377, L.381, F.387 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:Y.267, B:F.387 Hydrogen bonds: B:E.377

2 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.8: 8 residues within 4Å: Chain B: R.133, D.136, R.330, V.331, K.332, I.359, K.360, D.361 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:R.330, B:K.332, B:I.359, B:D.361 Hydrogen bonds: B:R.133, B:K.360 MRD.9: 9 residues within 4Å: Chain B: E.226, S.229, K.230, P.252, I.256, Y.284, R.297, V.298, E.301 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:P.252, B:I.256, B:V.298 Hydrogen bonds: B:S.229, B:R.297, B:E.301

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Brooks, M.A. et al., The structure of an archaeal homodimeric ligase which has RNA circularization activity. Protein Sci. (2008)

Release Date

2008-06-03

Peptides

PAB1020: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PAB1020