SMTL ID : 3kgd.1 (3 other biounits)

Crystal structure of E. coli RNA 3' cyclase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.68 Å

Oligo State

monomer

Ligands

1 x AMP: ADENOSINE MONOPHOSPHATE(Covalent)

AMP.1: 14 residues within 4Å: Chain A: Q.37, R.40, L.120, Q.123, P.147, S.148, A.149, P.150, F.154, F.270, Y.303, D.306, Q.307, H.328 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Q.37, A:Q.123, A:D.306, A:Q.307 Water bridges: A:Q.37, A:Q.123, A:S.148, A:F.270, A:Y.303, A:Y.303 Salt bridges: A:H.328 pi-Stacking: A:F.154, A:Y.303

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: G.35, G.36, R.40, Q.70, A.74, I.112, L.120, V.121 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.36, A:R.40, A:A.74 GOL.3: 6 residues within 4Å: Chain A: G.106, D.107, P.135, S.136, R.137, E.190 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.106, A:E.190 Water bridges: A:S.136

1 x NA: SODIUM ION(Non-functional Binders)

NA.4: 4 residues within 4Å: Chain A: E.33, G.36 Ligands: SO4.5, SO4.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.33 Water bridges: A:Q.37, A:R.40, A:R.40

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 4 residues within 4Å: Chain A: G.32, E.33, R.62 Ligands: NA.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.33 Water bridges: A:G.34, A:R.59 Salt bridges: A:R.62 SO4.6: 3 residues within 4Å: Chain A: Q.70, H.71 Ligands: NA.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.70 Water bridges: A:R.59, A:R.59 Salt bridges: A:H.71 SO4.7: 2 residues within 4Å: Chain A: S.237, H.239 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.237 Water bridges: A:S.237 Salt bridges: A:H.239

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tanaka, N. et al., Structure of the RNA 3'-phosphate cyclase-adenylate intermediate illuminates nucleotide specificity and covalent nucleotidyl transfer. Structure (2010)

Release Date

2010-04-21

Peptides

RNA 3'-terminal phosphate cyclase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

RNA 3'-terminal phosphate cyclase

Related Entries With Identical Sequence