SMTL ID : 6dw4.1

SAMHD1 Bound to Cladribine-TP in the Catalytic Pocket and Allosteric Pocket

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-tetramer

Ligands

8 x HF7: 2'-deoxy-2-methyladenosine 5'-(tetrahydrogen triphosphate)(Non-covalent)

HF7.1: 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.4 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:L.74, A:Y.298 Hydrogen bonds: A:Q.73, A:R.88, A:Q.299 Water bridges: A:R.130, A:R.130, A:R.130, A:R.130, A:R.130, A:R.130, A:R.130, A:R.130, A:R.130, A:N.131, A:M.140, A:E.158, A:R.290, A:R.290, A:R.290, A:Y.298, A:Q.299, A:Q.299 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 pi-Stacking: A:H.139 HF7.2: 20 residues within 4Å: Chain A: D.254, 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.6, GTP.7 22 PLIP interactions: 7 interactions with chain C, 13 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: C:V.80, C:F.81, C:I.249 Salt bridges: C:H.300, C:H.300, C:K.301, C:K.301, A:R.257, A:R.276, A:K.278, A:K.278, A:K.278, A:K.447 Hydrogen bonds: A:R.257, A:N.282, A:N.282, B:N.43, B:N.43 Water bridges: A:R.257, A:R.257 pi-Cation interactions: A:R.257, A:R.257 HF7.5: 18 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, NA.11 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:L.74, B:Y.298 Hydrogen bonds: B:Q.73, B:R.88, B:N.131, B:Y.239, B:Y.239, B:Q.299 Water bridges: B:R.88, B:R.130, B:R.130, B:R.130, B:R.144, B:D.235, B:K.236, B:R.290, B:R.290, B:R.290, B:Y.298, B:D.307, 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 pi-Stacking: B:H.139 HF7.8: 18 residues within 4Å: Chain A: V.41, I.42, N.43, H.49 Chain B: D.254, R.257, R.276, K.278, N.282, K.447 Chain D: V.80, F.81, G.248, I.249, R.296, H.300 Ligands: GTP.3, MG.9 30 PLIP interactions: 3 interactions with chain A, 17 interactions with chain B, 10 interactions with chain D Hydrogen bonds: A:N.43, A:N.43, B:R.257, B:N.282, B:N.282 Water bridges: A:K.40, B:R.257, B:R.257, B:R.257, B:R.257, B:R.276, B:R.276, B:R.276, D:H.300, D:K.301, D:K.301 Salt bridges: B:R.257, B:R.276, B:K.278, B:K.278, B:K.447, D:H.300, D:H.300, D:K.301, D:K.301 pi-Cation interactions: B:R.257, B:R.257 Hydrophobic interactions: D:V.80, D:F.81, D:I.249 HF7.12: 21 residues within 4Å: Chain A: V.80, F.81, G.248, I.249, R.296, H.300, K.301, V.302 Chain C: D.254, R.257, F.261, R.276, K.278, N.282, K.447 Chain D: V.41, I.42, N.43, H.49 Ligands: MG.16, GTP.17 31 PLIP interactions: 17 interactions with chain C, 12 interactions with chain A, 2 interactions with chain D Hydrogen bonds: C:R.257, C:N.282, C:N.282, D:N.43, D:N.43 Water bridges: C:R.257, C:R.257, C:R.257, C:R.257, C:K.278, C:K.278, A:K.301, A:K.301, A:K.301, A:K.301 Salt bridges: C:R.257, C:R.276, C:K.278, C:K.278, C:K.278, C:K.447, A:H.300, A:H.300, A:K.301, A:K.301, A:K.301 pi-Cation interactions: C:R.257, C:R.257 Hydrophobic interactions: A:V.80, A:F.81, A:I.249 HF7.14: 17 residues within 4Å: Chain C: 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.15 29 PLIP interactions: 29 interactions with chain C Hydrophobic interactions: C:L.74, C:Y.298 Hydrogen bonds: C:Q.73, C:R.88, C:N.131, C:Y.239, C:Q.299, C:Q.299 Water bridges: C:R.88, C:R.88, C:R.130, C:R.130, C:R.130, C:E.158, C:D.235, C:D.235, C:R.290, C:R.290, C:D.307 Salt bridges: C:R.88, C:R.130, C:H.134, C:H.139, C:H.139, C:H.157, C:H.157, C:K.236, C:R.290 pi-Stacking: C:H.139 HF7.18: 20 residues within 4Å: Chain B: V.80, F.81, I.249, R.296, H.300, K.301, V.302 Chain C: V.41, I.42, N.43, H.49 Chain D: D.254, R.257, F.261, R.276, K.278, N.282, K.447 Ligands: GTP.13, MG.19 30 PLIP interactions: 11 interactions with chain B, 17 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: B:V.80, B:F.81, B:I.249 Hydrogen bonds: B:R.296, D:R.257, D:N.282, C:N.43, C:N.43 Water bridges: B:K.301, B:K.301, D:R.257, D:R.257, D:R.257, D:R.257, D:R.276, D:R.276, D:K.447 Salt bridges: B:H.300, B:H.300, B:K.301, B:K.301, B:K.301, D:R.257, D:R.276, D:K.278, D:K.278, D:K.278, D:K.447 pi-Cation interactions: D:R.257, D:R.257 HF7.20: 17 residues within 4Å: Chain D: 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.21 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:L.74, D:Y.298 Hydrogen bonds: D:Q.73, D:R.88, D:Q.299, D:Q.299 Water bridges: D:R.88, D:R.88, D:R.130, D:R.130, D:R.130, D:R.130, D:N.131, D:K.236, D:K.236, D:R.290, 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 pi-Stacking: D:H.139

4 x GTP: GUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

GTP.3: 15 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 Ligands: HF7.8, MG.9 24 PLIP interactions: 14 interactions with chain A, 5 interactions with chain B, 5 interactions with chain D Hydrogen bonds: A:V.41, A:Q.66, A:R.69, D:R.375 Water bridges: A:K.40, A:K.40, A:K.40, A:K.40, A:K.40, A:D.61, A:Q.66, B:K.447, B:K.447, B:K.447, D:K.301 Salt bridges: A:K.40, A:K.40, A:K.40, A:D.61, B:K.447, B:K.447, D:K.301, D:R.375 pi-Cation interactions: D:R.375 GTP.7: 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: HF7.2, MG.6 16 PLIP interactions: 9 interactions with chain B, 5 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:V.41, B:Q.66, B:R.69, C:R.375 Water bridges: B:K.40, B:K.40 Salt bridges: B:K.40, B:K.40, B:K.40, B:D.61, C:R.375, C:K.379, C:K.379, A:K.447, A:K.447 pi-Cation interactions: C:R.375 GTP.13: 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: HF7.18, MG.19 20 PLIP interactions: 11 interactions with chain C, 7 interactions with chain B, 2 interactions with chain D Hydrogen bonds: C:V.41, C:Q.66, C:R.69, B:R.375 Water bridges: C:K.40, C:K.40, C:K.40, C:K.40, B:K.301, B:K.301 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 GTP.17: 16 residues within 4Å: Chain A: Y.79, V.80, V.302, R.375, K.379 Chain C: K.447 Chain D: K.40, V.41, I.42, I.60, D.61, Q.66, R.69, F.89 Ligands: HF7.12, MG.16 20 PLIP interactions: 7 interactions with chain A, 2 interactions with chain C, 11 interactions with chain D Hydrogen bonds: A:R.375, D:V.41, D:Q.66, D:R.69 Water bridges: A:K.301, A:K.379, D:K.40, D:K.40, D:K.40, D:D.61 Salt bridges: A:R.375, A:K.379, A:K.379, C:K.447, C:K.447, D:K.40, D:K.40, D:K.40, D:D.61 pi-Cation interactions: A:R.375

8 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 3 residues within 4Å: Chain A: R.130, K.236 Ligands: HF7.1 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain A: K.447 Chain B: K.40 Ligands: HF7.2, GTP.7 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain A: K.40 Chain B: K.447 Ligands: GTP.3, HF7.8 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain B: D.233, K.236 Ligands: HF7.5 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain C: D.233, K.236 Ligands: HF7.14 No protein-ligand interaction detected (PLIP) MG.16: 4 residues within 4Å: Chain C: K.447 Chain D: K.40 Ligands: HF7.12, GTP.17 No protein-ligand interaction detected (PLIP) MG.19: 4 residues within 4Å: Chain C: K.40 Chain D: K.447 Ligands: GTP.13, HF7.18 No protein-ligand interaction detected (PLIP) MG.21: 3 residues within 4Å: Chain D: D.233, K.236 Ligands: HF7.20 No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.11: 5 residues within 4Å: Chain B: L.74, G.77, A.297, Y.298 Ligands: HF7.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.297 Water bridges: B:H.300

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Knecht, K.M. et al., The structural basis for cancer drug interactions with the catalytic and allosteric sites of SAMHD1. Proc. Natl. Acad. Sci. U.S.A. (2018)

Release Date

2018-10-10

Peptides

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
C

C
B

D
A

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

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