SMTL ID : 4qfz.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-tetramer

Ligands

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

DGT.1: 15 residues within 4Å: Chain A: Y.79, V.80, V.302, R.375, K.379 Chain D: K.40, V.41, I.42, I.60, D.61, Q.66, R.69, F.89 Ligands: TTP.10, MG.21 11 PLIP interactions: 4 interactions with chain A, 7 interactions with chain D Salt bridges: A:R.375, A:K.379, A:K.379, D:K.40, D:K.40, D:K.40, D:D.61 pi-Cation interactions: A:R.375 Hydrophobic interactions: D:I.42 Hydrogen bonds: D:Q.66, D:R.69 DGT.11: 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, TTP.16 18 PLIP interactions: 2 interactions with chain D, 5 interactions with chain B, 11 interactions with chain C Salt bridges: D:K.447, D:K.447, B:R.375, B:K.379, B:K.379, C:K.40, C:K.40, C:K.40, C:D.61 Hydrogen bonds: B:R.375, C:Q.66, C:R.69 pi-Cation interactions: B:R.375 Hydrophobic interactions: C:I.42 Water bridges: C:K.40, C:K.40, C:K.40, C:K.40 DGT.12: 16 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, V.302, R.375, K.379 Ligands: TTP.3, MG.8 18 PLIP interactions: 2 interactions with chain A, 6 interactions with chain C, 10 interactions with chain B Salt bridges: A:K.447, A:K.447, C:R.375, C:K.379, C:K.379, B:K.40, B:K.40, B:K.40, B:D.61 Water bridges: C:K.379, C:K.379, B:K.40, B:K.40, B:D.61 pi-Cation interactions: C:R.375 Hydrophobic interactions: B:I.42 Hydrogen bonds: B:Q.66, B:R.69 DGT.17: 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.4, TTP.7 16 PLIP interactions: 10 interactions with chain A, 2 interactions with chain B, 4 interactions with chain D Hydrophobic interactions: A:I.42 Hydrogen bonds: A:Q.66, A:R.69 Water bridges: A:K.40, A:K.40, A:D.61 Salt bridges: A:K.40, A:K.40, A:K.40, A:D.61, B:K.447, B:K.447, D:R.375, D:K.379, D:K.379 pi-Cation interactions: D:R.375

8 x TTP: THYMIDINE-5'-TRIPHOSPHATE(Non-covalent)

TTP.2: 17 residues within 4Å: Chain A: 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.5 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:L.74, A:Y.298, A:Y.298 Hydrogen bonds: A:Q.73, A:R.88, A:Y.239, A:Q.299 Water bridges: A:R.130, A:R.130, A:R.290, A:R.290, A:R.290 Salt bridges: A:R.88, A:R.130, A:H.134, A:H.139, A:H.157, A:H.157, A:K.236, A:R.290 TTP.3: 19 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, I.249, R.296, H.300, K.301, V.302 Ligands: MG.8, DGT.12 18 PLIP interactions: 10 interactions with chain A, 7 interactions with chain C, 1 interactions with chain B Hydrogen bonds: A:R.257, A:R.257, A:N.282, B:N.43 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, C:K.301 pi-Cation interactions: A:R.257 Hydrophobic interactions: C:F.81, C:I.249 TTP.6: 15 residues within 4Å: Chain B: 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.9 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:L.74, B:Y.298, B:Y.298 Hydrogen bonds: B:Q.73, B:R.88, B:Y.239, B:Q.299 Water bridges: B:R.130, B:R.130, B:D.235, B:D.235, B:K.236, B:K.236, B:Y.239, B:R.290, B:D.307 Salt bridges: B:R.88, B:R.130, B:H.134, B:H.139, B:H.157, B:H.157, B:K.236, B:R.290 TTP.7: 17 residues within 4Å: Chain A: V.41, I.42, N.43, H.49 Chain B: R.257, R.276, K.278, N.282, K.447 Chain D: V.80, F.81, R.296, H.300, K.301, V.302 Ligands: MG.4, DGT.17 19 PLIP interactions: 8 interactions with chain D, 10 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: D:F.81 Hydrogen bonds: D:R.296, B:R.257, B:R.257, B:N.282, A:N.43 Water bridges: D:R.296 Salt bridges: D:H.300, D:H.300, D:K.301, 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 TTP.10: 18 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 Ligands: DGT.1, MG.21 19 PLIP interactions: 1 interactions with chain D, 8 interactions with chain A, 10 interactions with chain C Hydrogen bonds: D:N.43, C:R.257, C:R.257, C:N.282 Hydrophobic interactions: A:V.80, A:F.81, A:I.249 Salt bridges: A:H.300, A:H.300, A:K.301, A:K.301, A:K.301, C:R.257, C:R.276, C:K.278, C:K.278, C:K.278, C:K.447 pi-Cation interactions: C:R.257 TTP.13: 16 residues within 4Å: Chain C: 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.15 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:L.74, C:Y.298, C:Y.298 Hydrogen bonds: C:Q.73, C:R.88, C:Y.239, C:Q.299 Water bridges: C:R.130, C:R.130, C:R.130, C:E.158, C:D.235, C:Y.239, C:R.290 Salt bridges: C:R.88, C:R.130, C:H.134, C:H.139, C:H.157, C:H.157, C:K.236, C:R.290 TTP.16: 18 residues within 4Å: Chain B: V.80, F.81, R.296, H.300, K.301, 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.11, MG.14 18 PLIP interactions: 2 interactions with chain C, 10 interactions with chain D, 6 interactions with chain B Hydrogen bonds: C:V.41, C:N.43, D:R.257, D:R.257, D:N.282 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, B:K.301, B:K.301, B:K.301 pi-Cation interactions: D:R.257 Hydrophobic interactions: B:F.81 TTP.18: 15 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, Y.298, Q.299 Ligands: MG.19 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:L.74, D:Y.298, D:Y.298 Hydrogen bonds: D:Q.73, D:R.88, D:Q.299 Water bridges: D:R.130, D:R.130, D:R.130, D:Y.239, D:R.290 Salt bridges: D:R.88, D:R.130, D:H.134, D:H.139, D:H.157, D:H.157, D:K.236, D:R.290

9 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.4: 3 residues within 4Å: Chain A: K.40 Ligands: TTP.7, DGT.17 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain A: D.233, K.236 Ligands: TTP.2 No protein-ligand interaction detected (PLIP) MG.8: 3 residues within 4Å: Chain B: K.40 Ligands: TTP.3, DGT.12 No protein-ligand interaction detected (PLIP) MG.9: 2 residues within 4Å: Chain B: K.236 Ligands: TTP.6 No protein-ligand interaction detected (PLIP) MG.14: 2 residues within 4Å: Ligands: DGT.11, TTP.16 No protein-ligand interaction detected (PLIP) MG.15: 2 residues within 4Å: Chain C: K.236 Ligands: TTP.13 No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain D: K.236 Ligands: TTP.18 No protein-ligand interaction detected (PLIP) MG.20: 1 residues within 4Å: Chain D: K.329 No protein-ligand interaction detected (PLIP) MG.21: 3 residues within 4Å: Chain D: K.40 Ligands: DGT.1, TTP.10 No protein-ligand interaction detected (PLIP)

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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