SMTL ID : 8f5x.1

Crystal structure of human eosinophil-derived neurotoxin (EDN, ribonuclease 2) in complex with 5'-adenosine monophosphate (AMP)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

monomer

Ligands

3 x SIN: SUCCINIC ACID(Non-covalent)

SIN.1: 10 residues within 4Å: Chain A: T.47, N.51, V.52, V.55, N.58, S.75, G.76, S.77, V.79, Y.108 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.79 Hydrogen bonds: A:T.47, A:N.51, A:G.76, A:S.77, A:Y.108, A:Y.108 Water bridges: A:N.51, A:V.55, A:N.58 SIN.2: 4 residues within 4Å: Chain A: N.40, Q.41, L.86 Ligands: EDO.5 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:N.40, A:Q.41 Hydrogen bonds: A:N.40, A:N.40 SIN.6: 6 residues within 4Å: Chain A: Q.41, H.83, T.102, M.106, I.134 Ligands: EDO.7 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:I.134 Hydrogen bonds: A:Q.41 Salt bridges: A:H.83, A:H.83

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

EDO.3: 3 residues within 4Å: Chain A: S.65, N.66, K.67 No protein-ligand interaction detected (PLIP) EDO.5: 3 residues within 4Å: Chain A: Q.41, N.85 Ligands: SIN.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.41 EDO.7: 6 residues within 4Å: Chain A: S.65, L.131, D.132, R.133, I.134 Ligands: SIN.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.132, A:I.134, A:I.134 EDO.8: 2 residues within 4Å: Chain A: R.118, R.119 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.118, A:R.118

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.4: 8 residues within 4Å: Chain A: W.8, N.66, R.69, N.71, A.111, D.113, V.129, H.130 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.66, A:R.69, A:N.71 Water bridges: A:R.69 Salt bridges: A:R.69 pi-Stacking: A:W.8, A:W.8

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tran, T.T.Q. et al., Ancestral sequence reconstruction dissects structural and functional differences among eosinophil ribonucleases. J.Biol.Chem. (2024)

Release Date

2023-11-29

Peptides

Non-secretory ribonuclease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Non-secretory ribonuclease

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