SMTL ID : 6dw7.1

SAMHD1 without Catalytic Nucleotides

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-tetramer

Ligands

4 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.1: 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, P.82, R.296, H.300, K.301, V.302 Ligands: MG.7, GTP.8 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 Salt bridges: C:H.300, C:H.300, C:K.301, 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.276, A:K.447 pi-Cation interactions: A:R.257, A:R.257 DTP.9: 20 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, P.82, I.249, R.296, H.300, K.301, V.302 Ligands: MG.2, GTP.3 21 PLIP interactions: 13 interactions with chain B, 6 interactions with chain D, 2 interactions with chain A Hydrogen bonds: B:R.257, B:N.282, B:N.282, A:N.43, A:N.43 Water bridges: B:R.276, B:R.276 Salt bridges: B:R.257, B:R.276, B:K.278, 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 DTP.10: 18 residues within 4Å: Chain A: V.80, F.81, 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: MG.11, GTP.16 21 PLIP interactions: 6 interactions with chain A, 13 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: A:V.80, A:F.81 Salt bridges: A:H.300, A:H.300, A:K.301, A:K.301, C:R.257, C:R.276, C:K.278, C:K.278, C:K.278, C:K.447 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 pi-Cation interactions: C:R.257, C:R.257 DTP.17: 19 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: R.257, F.261, R.276, K.278, N.282, K.447 Ligands: MG.12, GTP.13 20 PLIP interactions: 11 interactions with chain D, 7 interactions with chain B, 2 interactions with chain C Hydrogen bonds: D:R.257, D:N.282, D:N.282, C:N.43, C:N.43 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, D:R.257 Hydrophobic interactions: B:V.80, B:F.81

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

MG.2: 3 residues within 4Å: Chain A: K.40 Ligands: GTP.3, DTP.9 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Ligands: DTP.1, GTP.8 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain D: K.40 Ligands: DTP.10, GTP.16 No protein-ligand interaction detected (PLIP) MG.12: 4 residues within 4Å: Chain C: K.40 Chain D: K.447 Ligands: GTP.13, DTP.17 No protein-ligand interaction detected (PLIP)

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: MG.2, DTP.9 12 PLIP interactions: 3 interactions with chain D, 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: D:R.375, A:K.40, A:K.40, A:V.41, A:Q.66, A:R.69 Salt bridges: D:R.375, A:K.40, A:D.61, B:K.447, B:K.447 pi-Cation interactions: D:R.375 GTP.8: 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: DTP.1, MG.7 17 PLIP interactions: 9 interactions with chain B, 6 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:K.40, B:K.40, B:V.41, B:Q.66, B:R.69, C:R.375 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 Water bridges: C:R.375 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: MG.12, DTP.17 14 PLIP interactions: 5 interactions with chain B, 7 interactions with chain C, 2 interactions with chain D Hydrogen bonds: B:R.375, C:V.41, C:Q.66, C:R.69 Salt bridges: B:R.375, B:K.379, B:K.379, C:K.40, C:K.40, C:K.40, C:D.61, D:K.447, D:K.447 pi-Cation interactions: B:R.375 GTP.16: 16 residues within 4Å: Chain A: Y.79, V.80, V.302, R.375, L.377 Chain C: K.447 Chain D: K.40, V.41, I.42, I.60, D.61, Q.66, R.69, F.89 Ligands: DTP.10, MG.11 13 PLIP interactions: 7 interactions with chain D, 4 interactions with chain A, 2 interactions with chain C Hydrogen bonds: D:V.41, D:Q.66, D:R.69, A:R.375 Salt bridges: D:K.40, D:K.40, D:K.40, D:D.61, A:R.375, A:K.379, C:K.447, C:K.447 pi-Cation interactions: A:R.375

2 x GLY: GLYCINE(Non-covalent)

GLY.4: 2 residues within 4Å: Chain A: G.432 Ligands: NA.5 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Ligand interactions Water bridges: A:K.236 Hydrogen bonds: G.4, G.4 GLY.14: 4 residues within 4Å: Chain C: H.139, K.236, Y.239, R.290 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:D.235, C:D.235, C:Y.239, C:Y.239 Salt bridges: C:K.236, C:R.290

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

NA.5: 4 residues within 4Å: Chain A: D.233, D.235, K.236 Ligands: GLY.4 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:R.130, A:D.235, G.4 NA.6: 5 residues within 4Å: Chain A: T.38, M.39, K.40, P.54, V.57 No protein-ligand interaction detected (PLIP) NA.15: 7 residues within 4Å: Chain C: D.430, Y.431, G.432, M.433, Q.434, K.436, F.469 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:Y.431, C:M.433, C:F.469

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.18: 4 residues within 4Å: Chain D: K.236, Y.239, R.290, H.294 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.239, D:Y.239 Salt bridges: D:K.236, D:R.290

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
A

B
B

C
C

D
D

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

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