SMTL ID : 4qg0.1

Crystal structure of the tetrameric dGTP/dUTP-bound SAMHD1 (RN206) mutant catalytic core

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

4 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.1: 16 residues within 4Å: Chain A: Y.79, V.80, V.302, R.375, K.379 Chain D: K.40, V.41, I.42, V.57, I.60, D.61, Q.66, R.69, F.89 Ligands: DUT.11, MG.18 16 PLIP interactions: 8 interactions with chain D, 6 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: D:I.42 Hydrogen bonds: D:Q.66, D:R.69, A:R.375 Water bridges: D:D.61 Salt bridges: D:K.40, D:K.40, D:K.40, D:D.61, A:K.301, A:R.375, A:K.379, A:K.379, C:K.447, C:K.447 pi-Cation interactions: A:R.375 DGT.7: 16 residues within 4Å: Chain B: Y.79, V.80, V.302, R.375, K.379 Chain C: K.40, V.41, I.42, I.60, D.61, Q.66, R.69, F.89 Chain D: K.447 Ligands: MG.14, DUT.15 16 PLIP interactions: 9 interactions with chain C, 5 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: C:I.42 Hydrogen bonds: C:Q.66, C:R.69, B:R.375 Water bridges: C:K.40, C:K.40 Salt bridges: C:K.40, C:K.40, C:K.40, C:D.61, B:R.375, B:K.379, B:K.379, D:K.447, D:K.447 pi-Cation interactions: B:R.375 DGT.12: 17 residues within 4Å: Chain A: K.447 Chain B: K.40, V.41, I.42, I.60, D.61, Q.66, R.69, F.89 Chain C: Y.79, V.80, K.301, V.302, R.375, K.379 Ligands: DUT.3, MG.4 16 PLIP interactions: 6 interactions with chain C, 8 interactions with chain B, 2 interactions with chain A Hydrogen bonds: C:R.375, B:Q.66, B:R.69 Salt bridges: C:K.301, C:R.375, C:K.379, C:K.379, B:K.40, B:K.40, B:K.40, B:D.61, A:K.447, A:K.447 pi-Cation interactions: C:R.375 Hydrophobic interactions: B:I.42 Water bridges: B:D.61 DGT.16: 16 residues within 4Å: Chain A: K.40, V.41, I.42, I.60, D.61, Q.66, R.69, F.89 Chain B: K.447 Chain D: Y.79, V.80, V.302, R.375, K.379 Ligands: MG.5, DUT.9 16 PLIP interactions: 5 interactions with chain D, 9 interactions with chain A, 2 interactions with chain B Hydrogen bonds: D:R.375, A:Q.66, A:R.69 Salt bridges: D:R.375, D:K.379, D:K.379, A:K.40, A:K.40, A:K.40, A:D.61, B:K.447, B:K.447 pi-Cation interactions: D:R.375 Hydrophobic interactions: A:I.42 Water bridges: A:K.40, A:K.40

8 x DUT: DEOXYURIDINE-5'-TRIPHOSPHATE(Non-covalent)

DUT.2: 15 residues within 4Å: Chain A: Q.73, L.74, R.88, R.130, H.134, H.139, H.157, D.235, K.236, Y.239, D.243, R.290, Y.298, Q.299 Ligands: MG.6 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.74, A:H.139, A:Y.298 Hydrogen bonds: A:Q.73, A:R.88, A:D.243, A:Y.298, A:Q.299 Water bridges: A:Y.239 Salt bridges: A:R.88, A:R.130, A:H.134, A:H.139, A:H.139, A:H.157, A:K.236, A:R.290 DUT.3: 18 residues within 4Å: Chain A: R.257, F.261, R.276, K.278, N.282, K.447 Chain B: V.41, I.42, N.43, H.49 Chain C: V.80, F.81, R.296, H.300, K.301, V.302 Ligands: MG.4, DGT.12 18 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B, 7 interactions with chain C Hydrogen bonds: A:R.257, A:N.282, B:N.43, B:N.43, C:V.80 Salt bridges: A:R.257, A:R.276, A:K.278, A:K.278, A:K.278, A:K.447, C:H.300, C:H.300, C:K.301, C:K.301 pi-Cation interactions: A:R.257 Hydrophobic interactions: C:V.80, C:F.81 DUT.8: 17 residues within 4Å: Chain B: Q.73, L.74, R.88, R.130, N.131, H.134, H.139, H.157, D.235, K.236, Y.239, D.243, R.290, H.294, Y.298, Q.299 Ligands: MG.10 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:L.74, B:H.139, B:Y.298 Hydrogen bonds: B:Q.73, B:R.88, B:Y.239, B:D.243, B:Y.298, B:Q.299 Water bridges: B:R.144 Salt bridges: B:R.88, B:R.130, B:H.134, B:H.139, B:H.139, B:H.157, B:H.157, B:K.236, B:R.290 DUT.9: 18 residues within 4Å: Chain A: V.41, I.42, N.43, H.49 Chain B: R.257, F.261, R.276, K.278, N.282, K.447 Chain D: V.80, F.81, R.296, H.300, K.301, V.302 Ligands: MG.5, DGT.16 18 PLIP interactions: 7 interactions with chain D, 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: D:V.80, D:F.81 Hydrogen bonds: D:V.80, B:R.257, B:N.282, A:N.43, A:N.43 Salt bridges: D:H.300, D:H.300, D:K.301, D:K.301, B:R.257, B:R.276, B:K.278, B:K.278, B:K.278, B:K.447 pi-Cation interactions: B:R.257 DUT.11: 19 residues within 4Å: Chain A: V.80, F.81, I.249, R.296, H.300, K.301, V.302 Chain C: R.257, F.261, R.276, K.278, N.282, K.447 Chain D: V.41, I.42, N.43, H.49 Ligands: DGT.1, MG.18 16 PLIP interactions: 7 interactions with chain C, 7 interactions with chain A, 2 interactions with chain D Hydrogen bonds: C:R.257, C:N.282, A:V.80, D:N.43, D:N.43 Salt bridges: C:R.257, C:R.276, C:K.278, C:K.447, A:H.300, A:H.300, A:K.301, A:K.301 pi-Cation interactions: C:R.257 Hydrophobic interactions: A:V.80, A:F.81 DUT.13: 14 residues within 4Å: Chain C: Q.73, L.74, R.88, R.130, H.134, H.139, H.157, D.233, D.235, K.236, Y.239, D.243, Y.298, Q.299 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:L.74, C:Y.298 Hydrogen bonds: C:Q.73, C:R.88, C:D.235, C:D.235, C:D.243, C:Y.298, C:Q.299 Water bridges: C:R.88, C:R.88, C:R.130, C:R.130 Salt bridges: C:R.88, C:R.130, C:R.130, C:H.134, C:H.139, C:H.139, C:H.157, C:H.157, C:K.236 DUT.15: 17 residues within 4Å: Chain B: V.80, F.81, R.296, H.300, V.302 Chain C: V.41, I.42, N.43, H.49 Chain D: R.257, F.261, R.276, K.278, N.282, K.447 Ligands: DGT.7, MG.14 18 PLIP interactions: 2 interactions with chain C, 11 interactions with chain D, 5 interactions with chain B Hydrogen bonds: C:N.43, C:N.43, D:R.257, D:N.282, B:V.80 Water bridges: D:K.278, D:K.278 Salt bridges: D:R.257, D:R.276, D:K.278, D:K.278, D:K.278, D:K.447, B:H.300, B:H.300 pi-Cation interactions: D:R.257 Hydrophobic interactions: B:V.80, B:F.81 DUT.17: 17 residues within 4Å: Chain D: Q.73, L.74, R.88, R.130, H.134, H.139, H.157, D.235, K.236, Y.239, D.243, R.290, H.294, Y.298, Q.299 Ligands: MG.19, EDO.20 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:L.74, D:Y.298 Hydrogen bonds: D:Q.73, D:R.88, D:Y.239, D:D.243, D:Y.298, D:Q.299 Water bridges: D:R.88, D:R.130, D:H.139 Salt bridges: D:R.88, D:R.130, D:R.130, D:H.134, D:H.139, D:H.139, D:H.157, D:H.157, D:K.236, D:R.290

7 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: K.447 Chain B: K.40 Ligands: DUT.3, DGT.12 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain A: K.40 Ligands: DUT.9, DGT.16 No protein-ligand interaction detected (PLIP) MG.6: 3 residues within 4Å: Chain A: R.130, K.236 Ligands: DUT.2 No protein-ligand interaction detected (PLIP) MG.10: 2 residues within 4Å: Chain B: R.130 Ligands: DUT.8 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain C: K.40 Ligands: DGT.7, DUT.15 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain D: K.40 Ligands: DGT.1, DUT.11 No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain D: R.130 Ligands: DUT.17 No protein-ligand interaction detected (PLIP)

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

EDO.20: 7 residues within 4Å: Chain D: L.74, Y.298, Q.299, G.303, N.304, D.307 Ligands: DUT.17 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Q.299, D:Q.299, D:N.304

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koharudin, L.M. et al., Structural Basis of Allosteric Activation of Sterile alpha Motif and Histidine-Aspartate Domain-containing Protein 1 (SAMHD1) by Nucleoside Triphosphates. J.Biol.Chem. (2014)

Release Date

2014-10-15

Peptides

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

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