SMTL ID : 6cm2.1

SAMHD1 HD domain bound to decitabine triphosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

homo-tetramer

Ligands

8 x F6G: 6-amino-3-{2-deoxy-5-O-[(R)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}phosphoryl]-beta-D-erythro-pentofuranosyl}-3,4-dihydro-1,3,5-triazin-2(1H)-one(Non-covalent)

F6G.1: 13 residues within 4Å: Chain A: Q.37, L.38, R.52, R.94, H.103, H.121, K.200, Y.203, D.207, R.254, H.258, Y.262, Q.263 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:L.38, A:Y.262 Hydrogen bonds: A:Q.37, A:R.52, A:D.207, A:Y.262, A:Q.263 Water bridges: A:R.94, A:R.94, A:R.94, A:N.95, A:Y.262, A:Q.263, A:N.268 Salt bridges: A:R.94, A:H.103, A:H.103, A:H.121, A:K.200, A:R.254, A:R.254, A:H.258 F6G.3: 17 residues within 4Å: Chain A: R.221, F.225, R.240, K.242, K.411 Chain B: V.5, I.6, N.7, H.13 Chain C: V.44, F.45, R.260, H.264, K.265, V.266 Ligands: MG.5, GTP.12 25 PLIP interactions: 9 interactions with chain C, 14 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: C:V.44, C:F.45 Hydrogen bonds: C:V.44, A:R.221, B:N.7, B:N.7 Water bridges: C:R.260, A:R.221, A:R.221, A:K.242, A:K.242, A:N.246 Salt bridges: C:H.264, C:H.264, C:K.265, C:K.265, C:K.265, A:R.221, A:R.240, A:K.242, A:K.242, A:K.242, A:E.243, A:K.411 pi-Cation interactions: A:R.221 F6G.4: 13 residues within 4Å: Chain B: Q.37, L.38, R.52, R.94, H.103, H.121, K.200, Y.203, D.207, R.254, H.258, Y.262, Q.263 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:L.38, B:Y.262 Hydrogen bonds: B:Q.37, B:R.52, B:Y.203, B:D.207, B:Y.262, B:Q.263 Water bridges: B:R.94, B:K.200, B:Y.262, B:N.268, B:D.271, B:D.271 Salt bridges: B:R.94, B:H.103, B:H.103, B:H.121, B:K.200, B:R.254, B:R.254, B:H.258 F6G.6: 17 residues within 4Å: Chain A: V.5, I.6, N.7, H.13 Chain B: R.221, F.225, R.240, K.242, K.411 Chain D: V.44, F.45, R.260, H.264, K.265, V.266 Ligands: MG.7, GTP.16 27 PLIP interactions: 16 interactions with chain B, 9 interactions with chain D, 2 interactions with chain A Hydrogen bonds: B:R.221, B:R.221, D:V.44, A:N.7, A:N.7 Water bridges: B:R.240, B:R.240, B:K.242, B:K.242, B:K.242, B:K.242, D:R.260 Salt bridges: B:R.221, B:R.240, B:K.242, B:K.242, B:K.242, B:E.243, B:K.411, D:H.264, D:H.264, D:K.265, D:K.265, D:K.265 pi-Cation interactions: B:R.221 Hydrophobic interactions: D:V.44, D:F.45 F6G.8: 17 residues within 4Å: Chain A: V.44, F.45, R.260, H.264, K.265, V.266 Chain C: R.221, F.225, R.240, K.242, K.411 Chain D: V.5, I.6, N.7, H.13 Ligands: GTP.2, MG.9 22 PLIP interactions: 13 interactions with chain C, 2 interactions with chain D, 7 interactions with chain A Hydrogen bonds: C:R.221, D:N.7, D:N.7, A:V.44 Water bridges: C:K.242, C:E.243, C:N.246, C:N.246 Salt bridges: C:R.221, C:R.240, C:K.242, C:K.242, C:K.242, C:E.243, C:K.411, A:H.264, A:H.264, A:K.265, A:K.265 pi-Cation interactions: C:R.221 Hydrophobic interactions: A:V.44, A:F.45 F6G.11: 13 residues within 4Å: Chain C: Q.37, L.38, R.52, R.94, H.103, H.121, K.200, Y.203, D.207, R.254, H.258, Y.262, Q.263 30 PLIP interactions: 30 interactions with chain C Hydrophobic interactions: C:L.38, C:Y.262 Hydrogen bonds: C:Q.37, C:R.52, C:Y.203, C:D.207, C:Y.262, C:Q.263 Water bridges: C:R.52, C:R.52, C:R.52, C:R.94, C:R.94, C:R.94, C:R.94, C:N.95, C:R.254, C:R.254, C:Y.262, C:Q.263, C:N.268, C:D.271 Salt bridges: C:R.94, C:H.103, C:H.103, C:H.121, C:K.200, C:R.254, C:R.254, C:H.258 F6G.13: 18 residues within 4Å: Chain B: V.44, F.45, R.260, H.264, K.265, V.266 Chain C: V.5, I.6, N.7, H.13 Chain D: R.221, F.225, R.240, K.242, N.246, K.411 Ligands: GTP.10, MG.14 25 PLIP interactions: 15 interactions with chain D, 8 interactions with chain B, 2 interactions with chain C Hydrogen bonds: D:R.221, D:N.246, B:V.44, C:N.7, C:N.7 Water bridges: D:R.221, D:R.221, D:R.221, D:K.242, D:K.242, B:R.260 Salt bridges: D:R.221, D:R.240, D:K.242, D:K.242, D:K.242, D:E.243, D:K.411, B:H.264, B:H.264, B:K.265, B:K.265 pi-Cation interactions: D:R.221 Hydrophobic interactions: B:V.44, B:F.45 F6G.15: 14 residues within 4Å: Chain D: Q.37, L.38, R.52, R.94, H.103, H.121, D.199, K.200, Y.203, D.207, R.254, H.258, Y.262, Q.263 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:L.38, D:Y.262 Hydrogen bonds: D:Q.37, D:R.52, D:E.122, D:D.207, D:Y.262, D:Q.263 Water bridges: D:R.94, D:R.94, D:Y.262, D:Q.263, D:N.268 Salt bridges: D:R.94, D:H.103, D:H.103, D:H.121, D:K.200, D:R.254, D:R.254, D:H.258

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

GTP.2: 16 residues within 4Å: Chain A: Y.43, V.44, V.266, R.339, K.343 Chain C: K.411 Chain D: K.4, V.5, I.6, I.24, D.25, Q.30, R.33, F.53 Ligands: F6G.8, MG.9 22 PLIP interactions: 2 interactions with chain C, 10 interactions with chain A, 10 interactions with chain D Salt bridges: C:K.411, C:K.411, A:K.265, A:R.339, A:K.343, A:K.343, D:K.4, D:K.4, D:K.4, D:D.25 Hydrogen bonds: A:R.339, D:V.5, D:Q.30, D:R.33 Water bridges: A:K.265, A:K.343, A:K.343, A:K.343, D:K.4, D:K.4, D:D.25 pi-Cation interactions: A:R.339 GTP.10: 16 residues within 4Å: Chain B: Y.43, V.44, V.266, R.339, K.343 Chain C: K.4, V.5, I.6, I.24, D.25, Q.30, R.33, F.53 Chain D: K.411 Ligands: F6G.13, MG.14 15 PLIP interactions: 10 interactions with chain C, 2 interactions with chain D, 3 interactions with chain B Hydrogen bonds: C:V.5, C:Q.30, C:R.33 Water bridges: C:K.4, C:K.4, C:Q.30 Salt bridges: C:K.4, C:K.4, C:K.4, C:D.25, D:K.411, D:K.411, B:R.339, B:K.343 pi-Cation interactions: B:R.339 GTP.12: 16 residues within 4Å: Chain A: K.411 Chain B: K.4, V.5, I.6, I.24, D.25, Q.30, R.33, F.53 Chain C: Y.43, V.44, V.266, R.339, K.343 Ligands: F6G.3, MG.5 17 PLIP interactions: 10 interactions with chain B, 5 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:V.5, B:Q.30, B:R.33, C:R.339 Water bridges: B:K.4, B:K.4, B:D.25 Salt bridges: B:K.4, B:K.4, B:K.4, B:D.25, C:R.339, C:K.343, C:K.343, A:K.411, A:K.411 pi-Cation interactions: C:R.339 GTP.16: 16 residues within 4Å: Chain A: K.4, V.5, I.6, I.24, D.25, Q.30, R.33, F.53 Chain B: K.411 Chain D: Y.43, V.44, V.266, R.339, K.343 Ligands: F6G.6, MG.7 16 PLIP interactions: 9 interactions with chain A, 5 interactions with chain D, 2 interactions with chain B Hydrogen bonds: A:V.5, A:Q.30, A:R.33, D:R.339 Water bridges: A:K.4, A:D.25 Salt bridges: A:K.4, A:K.4, A:K.4, A:D.25, D:R.339, D:K.343, D:K.343, B:K.411, B:K.411 pi-Cation interactions: D:R.339

4 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain B: K.4 Ligands: F6G.3, GTP.12 No protein-ligand interaction detected (PLIP) MG.7: 4 residues within 4Å: Chain A: K.4 Chain B: K.411 Ligands: F6G.6, GTP.16 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain C: K.411 Chain D: K.4 Ligands: GTP.2, F6G.8 No protein-ligand interaction detected (PLIP) MG.14: 4 residues within 4Å: Chain C: K.4 Chain D: K.411 Ligands: GTP.10, F6G.13 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oellerich, T. et al., Selective inactivation of hypomethylating agents by SAMHD1 provides a rationale for therapeutic stratification in AML. Nat Commun (2019)

Release Date

2019-06-19

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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