SMTL ID : 6yom.1

Crystal structure of tetrameric human D137N-SAMHD1 (residues 109-626) with XTP, dATP, dCMPNPP, Mn and Mg

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.25 Å

Oligo State

homo-tetramer

Ligands

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

FE.1: 6 residues within 4Å: Chain A: H.61, H.100, D.101, D.205 Ligands: MN.2, 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: 7 residues within 4Å: Chain B: R.58, H.61, H.100, D.101, D.205 Ligands: MN.10, 0KX.13 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.61, B:H.100, B:D.101, B:D.205 FE.15: 6 residues within 4Å: Chain C: H.61, H.100, D.101, D.205 Ligands: MN.16, 0KX.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: 7 residues within 4Å: Chain D: R.58, H.61, H.100, D.101, D.205 Ligands: MN.24, 0KX.27 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.61, D:H.100, D:D.101, D:D.205

4 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 5 residues within 4Å: Chain A: H.100, D.101, H.127 Ligands: FE.1, 0KX.5 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.101, A:H.127 MN.10: 5 residues within 4Å: Chain B: H.100, D.101, H.127 Ligands: FE.9, 0KX.13 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.101, B:H.127 MN.16: 5 residues within 4Å: Chain C: H.100, D.101, H.127 Ligands: FE.15, 0KX.19 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.101, C:H.127 MN.24: 5 residues within 4Å: Chain D: H.100, D.101, H.127 Ligands: FE.23, 0KX.27 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.101, D:H.127

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

MG.3: 4 residues within 4Å: Chain A: S.196, D.203, D.205 Ligands: 0KX.5 No protein-ligand interaction detected (PLIP) MG.4: 2 residues within 4Å: Ligands: CZF.6, DTP.8 No protein-ligand interaction detected (PLIP) MG.11: 5 residues within 4Å: Chain B: S.196, D.203, D.205, K.206 Ligands: 0KX.13 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain B: K.10 Ligands: DTP.7, CZF.14 No protein-ligand interaction detected (PLIP) MG.17: 4 residues within 4Å: Chain C: S.196, D.203, D.205 Ligands: 0KX.19 No protein-ligand interaction detected (PLIP) MG.18: 2 residues within 4Å: Ligands: CZF.20, DTP.22 No protein-ligand interaction detected (PLIP) MG.25: 5 residues within 4Å: Chain D: S.196, D.203, D.205, K.206 Ligands: 0KX.27 No protein-ligand interaction detected (PLIP) MG.26: 3 residues within 4Å: Chain D: K.10 Ligands: DTP.21, CZF.28 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, MN.2, MG.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.44, A:Y.268 Hydrogen bonds: A:Q.43, A:R.58, A:R.58, A:D.205, A:Y.209, A:Q.269 Salt bridges: A:K.206, A:R.260 pi-Stacking: A:H.109 0KX.13: 19 residues within 4Å: Chain B: 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.9, MN.10, MG.11 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:L.44, B:Y.268 Hydrogen bonds: B:Q.43, B:R.58, B:R.58, B:D.205, B:Y.209 Salt bridges: B:K.206, B:R.260 pi-Stacking: B:H.109 0KX.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 Ligands: FE.15, MN.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.100, C:D.205, C:Q.269 Salt bridges: C:K.206, C:R.260 pi-Stacking: C:H.109 0KX.27: 19 residues within 4Å: Chain D: 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.23, MN.24, MG.25 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:L.44, D:Y.268 Hydrogen bonds: D:Q.43, D:R.58, D:R.58, D:D.205 Salt bridges: D:K.206, D:R.260 pi-Stacking: D:H.109

4 x CZF: [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate(Non-covalent)

CZF.6: 17 residues within 4Å: Chain A: K.10, V.11, I.12, V.27, I.30, N.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.4, DTP.8 15 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B, 2 interactions with chain C Hydrogen bonds: A:K.10, A:K.10, A:V.11, A:N.31, A:N.31, A:Q.36, A:R.39, B:R.345 Salt bridges: A:K.10, B:R.345, B:K.349, C:K.417, C:K.417 pi-Cation interactions: B:R.345, B:R.345 CZF.14: 18 residues within 4Å: Chain A: Y.49, V.50, K.271, V.272, R.345, K.349 Chain B: K.10, V.11, I.12, V.27, I.30, N.31, Q.36, R.39, F.59 Chain D: K.417 Ligands: DTP.7, MG.12 18 PLIP interactions: 7 interactions with chain A, 2 interactions with chain D, 9 interactions with chain B Hydrogen bonds: A:V.50, A:R.345, A:R.345, B:K.10, B:K.10, B:V.11, B:N.31, B:N.31, B:Q.36, B:R.39 Salt bridges: A:K.271, A:R.345, A:K.349, D:K.417, D:K.417, B:K.10, B:K.10 pi-Cation interactions: A:R.345 CZF.20: 17 residues within 4Å: Chain A: K.417 Chain C: K.10, V.11, I.12, V.27, I.30, N.31, Q.36, R.39, F.59 Chain D: Y.49, V.50, V.272, R.345, K.349 Ligands: MG.18, DTP.22 15 PLIP interactions: 8 interactions with chain C, 5 interactions with chain D, 2 interactions with chain A Hydrogen bonds: C:K.10, C:K.10, C:V.11, C:N.31, C:N.31, C:Q.36, C:R.39, D:R.345 Salt bridges: C:K.10, D:R.345, D:K.349, A:K.417, A:K.417 pi-Cation interactions: D:R.345, D:R.345 CZF.28: 18 residues within 4Å: Chain B: K.417 Chain C: Y.49, V.50, K.271, V.272, R.345, K.349 Chain D: K.10, V.11, I.12, V.27, I.30, N.31, Q.36, R.39, F.59 Ligands: DTP.21, MG.26 18 PLIP interactions: 9 interactions with chain D, 7 interactions with chain C, 2 interactions with chain B Hydrogen bonds: D:K.10, D:K.10, D:V.11, D:N.31, D:N.31, D:Q.36, D:R.39, C:V.50, C:R.345, C:R.345 Salt bridges: D:K.10, D:K.10, C:K.271, C:R.345, C:K.349, B:K.417, B:K.417 pi-Cation interactions: C:R.345

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

DTP.7: 18 residues within 4Å: Chain A: V.50, F.51, P.52, R.266, H.270, K.271, V.272 Chain B: V.11, I.12, N.13, H.19 Chain D: R.227, R.246, K.248, N.252, K.417 Ligands: MG.12, CZF.14 20 PLIP interactions: 10 interactions with chain D, 8 interactions with chain A, 2 interactions with chain B Hydrogen bonds: D:R.227, D:N.252, A:R.266, 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 DTP.8: 17 residues within 4Å: Chain A: V.11, I.12, N.13, H.19 Chain B: V.50, F.51, R.266, H.270, K.271, V.272 Chain C: R.227, R.246, K.248, N.252, K.417 Ligands: MG.4, CZF.6 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.21: 18 residues within 4Å: Chain B: R.227, R.246, K.248, N.252, K.417 Chain C: V.50, F.51, P.52, R.266, H.270, K.271, V.272 Chain D: V.11, I.12, N.13, H.19 Ligands: MG.26, CZF.28 20 PLIP interactions: 10 interactions with chain B, 8 interactions with chain C, 2 interactions with chain D Hydrogen bonds: B:R.227, B:N.252, C:R.266, 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.22: 17 residues within 4Å: Chain A: R.227, R.246, K.248, N.252, K.417 Chain C: V.11, I.12, N.13, H.19 Chain D: V.50, F.51, R.266, H.270, K.271, V.272 Ligands: MG.18, CZF.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

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
A

B
B

C
A

D
B

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

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