SMTL ID : 8d9j.2 (1 other biounit)

SAMHD1-DNA complex

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.82 Å

Oligo State

homo-dimer

Ligands

3 x DT- DG: DNA (5'-D(*CP*AP*AP*TP*G)-3')(Non-covalent)

DT-DG.1: 1 residues within 4Å: Chain A: K.523 Protein-ligand interaction information (PLIP) not available DT-DG.2: 16 residues within 4Å: Chain A: Y.155, V.156, V.378, R.451, L.453, K.455 Chain B: T.114, K.116, V.117, I.118, V.133, I.136, D.137, Q.142, R.145, F.165 Protein-ligand interaction information (PLIP) not available DT-DG.3: 17 residues within 4Å: Chain A: K.116, V.117, I.118, V.133, I.136, D.137, Q.142, R.145, F.165 Chain B: Y.155, V.156, V.378, R.451, N.452, L.453, K.455, R.559 Protein-ligand interaction information (PLIP) not available

2 x FE: FE (III) ION(Non-covalent)

FE.4: 5 residues within 4Å: Chain A: R.164, H.167, H.206, D.207, D.311 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.167, A:H.206, A:D.207, A:D.311, A:D.311 FE.6: 6 residues within 4Å: Chain B: R.164, H.167, H.206, D.207, D.311 Ligands: CA.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.167, B:H.206, B:D.207, B:D.311

2 x CA: CALCIUM ION(Non-covalent)

CA.5: 4 residues within 4Å: Chain A: D.207, H.233, E.234, D.311 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.233, H2O.1, H2O.1 CA.7: 4 residues within 4Å: Chain B: H.206, D.207, H.233 Ligands: FE.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.207, B:H.233, H2O.3, H2O.4

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Simermeyer, T.L. et al., Protein oxidation increases SAMHD1 binding ssDNA via its regulatory site. Nucleic Acids Res. (2023)

Release Date

2023-07-05

Peptides

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
C

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

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