SMTL ID : 5hhj.1

Reverse transcriptase domain of group II intron maturase from Roseburia intestinalis in P21 space group

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-dimer

Ligands

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 4 residues within 4Å: Chain A: R.70, S.181, K.185 Ligands: SIN.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.181 Water bridges: A:K.185, A:K.185 Salt bridges: A:R.70, A:K.185 PO4.7: 3 residues within 4Å: Chain B: R.70, S.181, K.185 3 PLIP interactions: 3 interactions with chain B Water bridges: B:K.185 Salt bridges: B:R.70, B:K.185

2 x K: POTASSIUM ION(Non-covalent)

K.2: 6 residues within 4Å: Chain A: D.151, I.152, D.153, D.239, C.240, I.241 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.151, A:I.152, A:D.239, A:C.240, H2O.4 K.8: 6 residues within 4Å: Chain B: D.151, I.152, D.153, D.239, C.240, I.241 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.151, B:I.152, B:D.239, B:C.240, H2O.28

3 x GLY: GLYCINE(Non-covalent)

GLY.3: 7 residues within 4Å: Chain A: L.28, L.56, A.57, G.60, E.61, K.64, F.101 4 PLIP interactions: 4 interactions with chain A Water bridges: A:L.56, A:E.61, A:K.64 Salt bridges: A:K.64 GLY.4: 5 residues within 4Å: Chain A: Y.55, N.59, I.62, I.63, Q.66 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.55, A:Q.66 Water bridges: A:Q.66 GLY.9: 5 residues within 4Å: Chain B: Q.34, Q.104, A.107, Q.108, T.111 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.104, B:T.111

1 x SIN: SUCCINIC ACID(Non-covalent)

SIN.5: 3 residues within 4Å: Chain A: R.70, G.177 Ligands: PO4.1 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.70, A:R.70, A:D.178 Salt bridges: A:R.70

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

MPD.6: 9 residues within 4Å: Chain A: I.82, P.83, K.84, P.85 Chain B: Y.290, Y.291, D.292, T.293, S.294 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.290, A:P.83, A:P.85 Hydrogen bonds: B:Y.291, B:D.292, B:T.293

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhao, C. et al., Crystal structures of a group II intron maturase reveal a missing link in spliceosome evolution. Nat.Struct.Mol.Biol. (2016)

Release Date

2016-05-04

Peptides

Retron-type reverse transcriptase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Retron-type reverse transcriptase

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