SMTL ID : 6txe.3 (3 other biounits)

Crystal structure of tetrameric human wt-SAMHD1 (residues 109-626) with GTP, dATP, dTMPNPP and Mg

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.19 Å

Oligo State

homo-tetramer

Ligands

4 x FE: FE (III) ION(Non-covalent)

FE.1: 6 residues within 4Å: Chain A: R.58, H.61, H.100, D.101, D.205 Ligands: 1FZ.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.61, A:H.100, A:D.101, A:D.205 FE.9: 6 residues within 4Å: Chain B: R.58, H.61, H.100, D.101, D.205 Ligands: 1FZ.12 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.61, B:H.100, B:D.101, B:D.205 FE.16: 6 residues within 4Å: Chain C: R.58, H.61, H.100, D.101, D.205 Ligands: 1FZ.19 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.61, C:H.100, C:D.101, C:D.205 FE.23: 6 residues within 4Å: Chain D: R.58, H.61, H.100, D.101, D.205 Ligands: 1FZ.26 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.61, D:H.100, D:D.101, D:D.205

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: S.196, D.203, K.206 Ligands: 1FZ.4 No protein-ligand interaction detected (PLIP) MG.3: 3 residues within 4Å: Chain A: K.10 Ligands: GTP.5, DTP.15 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain B: D.203, D.205, K.206 Ligands: 1FZ.12 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain B: K.10 Ligands: GTP.7, DTP.22 No protein-ligand interaction detected (PLIP) MG.17: 5 residues within 4Å: Chain C: S.196, D.203, D.205, K.206 Ligands: 1FZ.19 No protein-ligand interaction detected (PLIP) MG.18: 3 residues within 4Å: Chain C: K.10 Ligands: DTP.8, GTP.20 No protein-ligand interaction detected (PLIP) MG.24: 4 residues within 4Å: Chain D: S.196, D.203, K.206 Ligands: 1FZ.26 No protein-ligand interaction detected (PLIP) MG.25: 3 residues within 4Å: Chain D: K.10 Ligands: DTP.14, GTP.27 No protein-ligand interaction detected (PLIP)

4 x 1FZ: 5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine(Non-covalent)

1FZ.4: 19 residues within 4Å: Chain A: Q.43, L.44, R.58, H.61, D.101, H.104, H.109, H.127, D.205, K.206, Y.209, D.213, R.260, H.264, Y.268, Q.269, D.277 Ligands: FE.1, MG.2 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.44, A:H.109, A:Y.268 Hydrogen bonds: A:Q.43, A:R.58, A:R.58, A:H.104, A:Y.209, A:D.213, A:Q.269, A:D.277 Salt bridges: A:K.206, A:R.260 1FZ.12: 19 residues within 4Å: Chain B: Q.43, L.44, R.58, H.61, H.100, D.101, H.104, H.109, H.127, D.205, K.206, Y.209, D.213, R.260, Y.268, Q.269, D.277 Ligands: FE.9, MG.10 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.268, B:Y.268 Hydrogen bonds: B:Q.43, B:R.58, B:R.58, B:H.104, B:H.127, B:Y.209, B:D.213, B:Q.269 Salt bridges: B:K.206, B:R.260 1FZ.19: 19 residues within 4Å: Chain C: Q.43, L.44, R.58, H.61, D.101, H.104, H.109, H.127, D.205, K.206, Y.209, D.213, R.260, H.264, Y.268, Q.269, D.277 Ligands: FE.16, MG.17 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:L.44, C:Y.268 Hydrogen bonds: C:Q.43, C:R.58, C:R.58, C:H.104, C:Y.209, C:D.213, C:Q.269 Salt bridges: C:K.206, C:R.260 1FZ.26: 20 residues within 4Å: Chain D: Q.43, L.44, R.58, H.61, H.100, D.101, H.104, H.109, H.127, D.205, K.206, Y.209, D.213, R.260, H.264, Y.268, Q.269, D.277 Ligands: FE.23, MG.24 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:Y.268 Hydrogen bonds: D:Q.43, D:R.58, D:R.58, D:H.104, D:Y.209, D:Y.209, D:D.213, D:Q.269, D:N.274 Salt bridges: D:K.206, D:R.260

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

GTP.5: 16 residues within 4Å: Chain A: K.10, V.11, I.12, I.30, D.31, Q.36, R.39, F.59 Chain B: Y.49, V.50, V.272, R.345, K.349 Chain C: K.417 Ligands: MG.3, DTP.15 16 PLIP interactions: 2 interactions with chain C, 5 interactions with chain B, 9 interactions with chain A Salt bridges: C:K.417, C:K.417, B:K.271, B:R.345, B:K.349, A:K.10, A:K.10, A:K.10, A:D.31 Hydrogen bonds: B:R.345, A:K.10, A:K.10, A:V.11, A:Q.36, A:R.39 pi-Cation interactions: B:R.345 GTP.7: 17 residues within 4Å: Chain A: Y.49, V.50, V.272, R.345, K.349 Chain B: K.10, V.11, I.12, V.27, I.30, D.31, Q.36, R.39, F.59 Chain D: K.417 Ligands: MG.11, DTP.22 16 PLIP interactions: 2 interactions with chain D, 7 interactions with chain A, 7 interactions with chain B Salt bridges: D:K.417, D:K.417, A:R.345, A:K.349, A:K.349, B:K.10, B:K.10, B:K.10, B:D.31 Hydrogen bonds: A:R.345, A:R.345, B:V.11, B:Q.36, B:R.39 pi-Cation interactions: A:R.345, A:R.345 GTP.20: 16 residues within 4Å: Chain A: K.417 Chain C: K.10, V.11, I.12, V.27, I.30, D.31, Q.36, R.39, F.59 Chain D: Y.49, V.50, V.272, R.345 Ligands: DTP.8, MG.18 17 PLIP interactions: 9 interactions with chain C, 6 interactions with chain D, 2 interactions with chain A Hydrogen bonds: C:K.10, C:K.10, C:V.11, C:Q.36, C:R.39, D:R.345 Salt bridges: C:K.10, C:K.10, C:K.10, C:D.31, D:K.271, D:R.345, D:K.349, A:K.417, A:K.417 pi-Cation interactions: D:R.345, D:R.345 GTP.27: 16 residues within 4Å: Chain B: K.417 Chain C: Y.49, V.50, V.272, R.345, K.349 Chain D: K.10, V.11, I.12, I.30, D.31, Q.36, R.39, F.59 Ligands: DTP.14, MG.25 15 PLIP interactions: 4 interactions with chain C, 2 interactions with chain B, 9 interactions with chain D Hydrogen bonds: C:R.345, D:K.10, D:K.10, D:V.11, D:Q.36, D:R.39 Salt bridges: C:R.345, C:K.349, B:K.417, B:K.417, D:K.10, D:K.10, D:K.10, D:D.31 pi-Cation interactions: C:R.345

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 3 residues within 4Å: Chain A: R.199, H.411, R.425 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.199 Salt bridges: A:H.411, A:R.425 SO4.13: 4 residues within 4Å: Chain B: R.199, R.242, H.411, R.425 4 PLIP interactions: 4 interactions with chain B Salt bridges: B:R.199, B:R.242, B:H.411, B:R.425 SO4.21: 4 residues within 4Å: Chain C: R.199, R.242, H.411, R.425 4 PLIP interactions: 4 interactions with chain C Salt bridges: C:R.199, C:R.242, C:H.411, C:R.425

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

DTP.8: 18 residues within 4Å: Chain A: R.227, F.231, R.246, K.248, N.252, K.417 Chain C: V.11, I.12, N.13, H.19 Chain D: V.50, F.51, I.219, R.266, H.270, K.271 Ligands: MG.18, GTP.20 20 PLIP interactions: 10 interactions with chain A, 8 interactions with chain D, 2 interactions with chain C Hydrogen bonds: A:R.227, A:N.252, D:R.266, C:N.13, C:N.13 Salt bridges: A:R.227, A:R.246, A:K.248, A:K.248, A:K.248, A:K.417, D:H.270, D:H.270, D:K.271, D:K.271, D:K.271 pi-Cation interactions: A:R.227, A:R.227 Hydrophobic interactions: D:V.50, D:F.51 DTP.14: 16 residues within 4Å: Chain B: R.227, R.246, K.248, N.252, K.417 Chain C: V.50, F.51, R.266, H.270, K.271 Chain D: V.11, I.12, N.13, H.19 Ligands: MG.25, GTP.27 20 PLIP interactions: 8 interactions with chain C, 10 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: C:V.50, C:F.51 Hydrogen bonds: C:R.266, B:R.227, B:N.252, D:N.13, D:N.13 Salt bridges: C:H.270, C:H.270, C:K.271, C:K.271, C:K.271, B:R.227, B:R.246, B:K.248, B:K.248, B:K.248, B:K.417 pi-Cation interactions: B:R.227, B:R.227 DTP.15: 18 residues within 4Å: Chain A: V.11, I.12, N.13, H.19 Chain B: V.50, F.51, I.219, R.266, H.270, K.271, V.272 Chain C: R.227, R.246, K.248, N.252, K.417 Ligands: MG.3, GTP.5 20 PLIP interactions: 8 interactions with chain B, 10 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: B:V.50, B:F.51 Hydrogen bonds: B:R.266, C:R.227, C:N.252, A:N.13, A:N.13 Salt bridges: B:H.270, B:H.270, B:K.271, B:K.271, B:K.271, C:R.227, C:R.246, C:K.248, C:K.248, C:K.248, C:K.417 pi-Cation interactions: C:R.227, C:R.227 DTP.22: 18 residues within 4Å: Chain A: V.50, F.51, I.219, R.266, H.270, K.271, V.272 Chain B: V.11, I.12, N.13 Chain D: R.227, F.231, R.246, K.248, N.252, K.417 Ligands: GTP.7, MG.11 20 PLIP interactions: 11 interactions with chain D, 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: D:R.227, D:N.252, D:N.252, B:N.13, B:N.13 Salt bridges: D:R.227, D:R.246, D:K.248, D:K.248, D:K.248, D:K.417, A:H.270, A:H.270, A:K.271, A:K.271, A:K.271 pi-Cation interactions: D:R.227, D:R.227 Hydrophobic interactions: A:V.50, A:F.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Morris, E.R. et al., Crystal structures of SAMHD1 inhibitor complexes reveal the mechanism of water-mediated dNTP hydrolysis. Nat Commun (2020)

Release Date

2020-06-24

Peptides

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
I

B
J

C
K

D
L

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

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