SMTL ID : 7n8w.1

Crystal structure of ERI2 nuclease bound to rAMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 15 residues within 4Å: Chain A: D.62, F.63, E.64, S.65, T.66, C.67, F.113, L.117, T.118, W.176 Chain B: K.72, H.73, H.74, H.75 Ligands: MN.3 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:K.72, B:H.74, A:D.62, A:E.64, A:E.64, A:S.65, A:S.65, A:N.69 Salt bridges: B:H.73, B:H.75

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

SO4.2: 7 residues within 4Å: Chain A: L.218, S.219, L.222, F.229, E.233, A.234, N.242 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.233, A:A.234, A:N.242 SO4.4: 6 residues within 4Å: Chain A: K.72, H.73, H.74 Chain B: W.173, R.204, G.217 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:W.173, B:G.217, A:H.74 Salt bridges: B:R.204, A:H.73 SO4.5: 6 residues within 4Å: Chain A: R.204 Chain B: H.73, H.74, H.75, S.76, H.107 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:H.75, B:S.76, B:S.76 Salt bridges: B:H.75, B:H.107, A:R.204 SO4.6: 6 residues within 4Å: Chain A: H.74, H.75, S.76, H.107 Chain B: R.204, K.208 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:H.74, A:S.76 Salt bridges: A:H.107, B:R.204, B:K.208

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.3: 3 residues within 4Å: Chain A: D.62 Chain B: H.75 Ligands: AMP.1 3 PLIP interactions: 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: H2O.1, H2O.1, AMP.1

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 2 residues within 4Å: Chain B: N.69, F.113 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thapar, R. et al., Crystal structure of ERI2 nuclease bound to rAMP. To Be Published

Release Date

2022-07-06

Peptides

ERI1 exoribonuclease 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ERI1 exoribonuclease 2

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