SMTL ID : 5dk5.1

Crystal structure of CRN-4-MES complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: R.146, C.220, C.270, Y.272, C.273, C.280 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.220, A:C.270, A:C.273, A:C.280 ZN.7: 6 residues within 4Å: Chain B: R.146, C.220, C.270, Y.272, C.273, C.280 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.220, B:C.270, B:C.273, B:C.280

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.2: 11 residues within 4Å: Chain A: E.27, F.81, T.82, T.171, I.173, H.189, D.190, A.191, D.193, D.194 Ligands: MG.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:F.81, A:T.171 Water bridges: A:D.121, A:I.173 Salt bridges: A:E.27, A:D.194 MES.8: 12 residues within 4Å: Chain B: E.27, F.81, T.82, T.171, I.173, H.189, D.190, A.191, D.193, D.194 Ligands: MG.9, IPA.13 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:T.171, B:T.171 Water bridges: B:D.121, B:N.172 Salt bridges: B:E.27, B:D.194

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: D.25, E.27, D.194 Ligands: MES.2 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.194, H2O.1, H2O.4, H2O.7, H2O.7 MG.9: 4 residues within 4Å: Chain B: D.25, E.27, D.194 Ligands: MES.8 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.25, H2O.12, H2O.13, H2O.16, H2O.17

7 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.4: 4 residues within 4Å: Chain A: A.169, T.170, T.171, G.174 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:A.169 Hydrogen bonds: A:T.170, A:T.170, A:T.171 IPA.5: 3 residues within 4Å: Chain A: W.224, K.244, E.247 No protein-ligand interaction detected (PLIP) IPA.6: 10 residues within 4Å: Chain A: R.225, R.226, Q.227, P.228, R.248, Q.286, T.287, P.288, H.289, D.290 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Q.286 Water bridges: A:R.248, A:D.290 IPA.10: 9 residues within 4Å: Chain B: D.121, S.122, R.123, Q.124, N.150, Y.152, K.153, N.172 Ligands: IPA.13 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.152 Hydrogen bonds: B:R.123, B:R.123, B:N.150 IPA.11: 8 residues within 4Å: Chain B: Y.37, P.38, C.39, R.128, Y.132, F.246, L.250, F.301 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:R.128, B:Y.132, B:F.246, B:F.301, B:F.301 Hydrogen bonds: B:R.128 Water bridges: B:Y.37 IPA.12: 10 residues within 4Å: Chain B: R.225, R.226, Q.227, P.228, R.248, Q.286, T.287, P.288, H.289, D.290 1 PLIP interactions: 1 interactions with chain B Water bridges: B:H.289 IPA.13: 8 residues within 4Å: Chain B: D.121, S.122, Q.124, T.171, N.172, I.173 Ligands: MES.8, IPA.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.121, B:N.172 Water bridges: B:D.121

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, K.-W. et al., Identification of Inhibitors for the DEDDh Family of Exonucleases and a Unique Inhibition Mechanism by Crystal Structure Analysis of CRN-4 Bound with 2-Morpholin-4-ylethanesulfonate (MES). J.Med.Chem. (2016)

Release Date

2016-08-24

Peptides

Cell death-related nuclease 4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Cell death-related nuclease 4

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