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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.84 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: 0KX.5 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: 0KX.12 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.61, B:H.100, B:D.101, B:D.205 FE.17: 7 residues within 4Å: Chain C: R.58, H.61, H.100, D.101, D.205 Ligands: MG.18, 0KX.21 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.61, C:H.100, C:D.101, C:D.205 FE.24: 6 residues within 4Å: Chain D: R.58, H.61, H.100, D.101, D.205 Ligands: 0KX.28 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.61, D:H.100, D:D.101, D:D.205

11 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: H.100, D.101, H.127 Ligands: 0KX.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.101, A:H.127 MG.3: 3 residues within 4Å: Chain A: D.203, K.206 Ligands: 0KX.5 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain A: K.10 Ligands: GTP.6, DTP.16 No protein-ligand interaction detected (PLIP) MG.10: 3 residues within 4Å: Chain B: D.203, K.206 Ligands: 0KX.12 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain B: K.10 Ligands: GTP.13, DTP.23 No protein-ligand interaction detected (PLIP) MG.18: 5 residues within 4Å: Chain C: H.100, D.101, H.127 Ligands: FE.17, 0KX.21 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.101, C:H.127 MG.19: 3 residues within 4Å: Chain C: D.203, K.206 Ligands: 0KX.21 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain C: K.10 Ligands: DTP.8, GTP.22 No protein-ligand interaction detected (PLIP) MG.25: 5 residues within 4Å: Chain D: H.100, D.101, H.127, E.128 Ligands: 0KX.28 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.101, D:H.127 MG.26: 3 residues within 4Å: Chain D: D.203, K.206 Ligands: 0KX.28 No protein-ligand interaction detected (PLIP) MG.27: 3 residues within 4Å: Chain D: K.10 Ligands: DTP.15, GTP.29 No protein-ligand interaction detected (PLIP)

4 x 0KX: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine(Non-covalent)

0KX.5: 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 Ligands: FE.1, MG.2, MG.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.268 Hydrogen bonds: A:Q.43, A:R.58, A:R.58, A:D.101, A:D.213 Salt bridges: A:K.206, A:R.260 pi-Stacking: A:H.109 0KX.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, H.264, Y.268, Q.269 Ligands: FE.9, MG.10 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:Y.268 Hydrogen bonds: B:Q.43, B:R.58, B:R.58, B:D.101, B:Y.209 Salt bridges: B:K.206, B:R.260 pi-Stacking: B:H.109 0KX.21: 20 residues within 4Å: Chain C: 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 Ligands: FE.17, MG.18, MG.19 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:L.44, C:Y.268 Hydrogen bonds: C:Q.43, C:R.58, C:R.58, C:D.205 Salt bridges: C:K.206, C:R.260 pi-Stacking: C:H.109 0KX.28: 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 Ligands: FE.24, MG.25, MG.26 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:Y.268 Hydrogen bonds: D:Q.43, D:R.58, D:R.58, D:D.205, D:Y.209 Salt bridges: D:K.206, D:R.260 pi-Stacking: D:H.109

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

GTP.6: 15 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 Chain C: K.417 Ligands: MG.4, DTP.16 13 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B, 2 interactions with chain C Hydrogen bonds: A:V.11, A:Q.36, A:R.39, B:R.345 Salt bridges: A:K.10, A:K.10, A:K.10, A:D.31, B:R.345, B:K.349, C:K.417, C:K.417 pi-Cation interactions: B:R.345 GTP.13: 16 residues within 4Å: Chain A: Y.49, V.50, V.272, R.345, K.349 Chain B: K.10, V.11, I.12, I.30, D.31, Q.36, R.39, F.59 Chain D: K.417 Ligands: MG.11, DTP.23 14 PLIP interactions: 7 interactions with chain B, 5 interactions with chain A, 2 interactions with chain D Hydrogen bonds: B:V.11, B:Q.36, B:R.39, A:R.345 Salt bridges: B:K.10, B:K.10, B:K.10, B:D.31, A:R.345, A:K.349, A:K.349, D:K.417, D:K.417 pi-Cation interactions: A:R.345 GTP.22: 15 residues within 4Å: Chain A: K.417 Chain C: K.10, V.11, I.12, I.30, D.31, Q.36, R.39, F.59 Chain D: Y.49, V.50, V.272, R.345 Ligands: DTP.8, MG.20 13 PLIP interactions: 7 interactions with chain C, 4 interactions with chain D, 2 interactions with chain A Hydrogen bonds: 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:R.345, D:K.349, A:K.417, A:K.417 pi-Cation interactions: D:R.345 GTP.29: 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.15, MG.27 14 PLIP interactions: 7 interactions with chain D, 2 interactions with chain B, 5 interactions with chain C Hydrogen bonds: D:V.11, D:Q.36, D:R.39, C:R.345 Salt bridges: D:K.10, D:K.10, D:K.10, D:D.31, B:K.417, B:K.417, C:R.345, C:K.349, C:K.349 pi-Cation interactions: C:R.345

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

SO4.7: 4 residues within 4Å: Chain A: R.199, R.242, H.411, R.425 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.411 Salt bridges: A:R.199, A:R.242, A:H.411, A:R.425 SO4.14: 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 SO4.30: 4 residues within 4Å: Chain D: R.199, R.242, H.411, R.425 4 PLIP interactions: 4 interactions with chain D Salt bridges: D:R.199, D:R.242, D:H.411, D:R.425

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

DTP.8: 17 residues within 4Å: Chain A: R.227, F.231, R.246, K.248, N.252, K.417 Chain C: V.11, N.13, H.19 Chain D: V.50, F.51, I.219, R.266, H.270, K.271 Ligands: MG.20, GTP.22 20 PLIP interactions: 11 interactions with chain A, 7 interactions with chain D, 2 interactions with chain C Hydrogen bonds: A:R.227, A:N.252, A:N.252, 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.15: 19 residues within 4Å: Chain B: R.227, F.231, R.246, K.248, N.252, K.417 Chain C: V.50, F.51, I.219, R.266, H.270, K.271, V.272 Chain D: V.11, I.12, N.13, H.19 Ligands: MG.27, GTP.29 20 PLIP interactions: 11 interactions with chain B, 7 interactions with chain C, 2 interactions with chain D Hydrogen bonds: B:R.227, B:N.252, B:N.252, D:N.13, D:N.13 Salt bridges: B:R.227, B:R.246, B:K.248, B:K.248, B:K.248, B:K.417, C:H.270, C:H.270, C:K.271, C:K.271, C:K.271 pi-Cation interactions: B:R.227, B:R.227 Hydrophobic interactions: C:V.50, C:F.51 DTP.16: 19 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, F.231, R.246, K.248, N.252, K.417 Ligands: MG.4, GTP.6 20 PLIP interactions: 7 interactions with chain B, 11 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: B:V.50, B:F.51 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 Hydrogen bonds: C:R.227, C:N.252, C:N.252, A:N.13, A:N.13 pi-Cation interactions: C:R.227, C:R.227 DTP.23: 19 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, H.19 Chain D: R.227, F.231, R.246, K.248, N.252, K.417 Ligands: MG.11, GTP.13 20 PLIP interactions: 2 interactions with chain B, 7 interactions with chain A, 11 interactions with chain D Hydrogen bonds: B:N.13, B:N.13, D:R.227, D:N.252, D:N.252 Hydrophobic interactions: A:V.50, A:F.51 Salt bridges: A:H.270, A:H.270, A:K.271, A:K.271, A:K.271, D:R.227, D:R.246, D:K.248, D:K.248, D:K.248, D:K.417 pi-Cation interactions: D:R.227, D:R.227

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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