SMTL ID : 6txa.4 (3 other biounits)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

homo-tetramer

Ligands

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

FE.1: 7 residues within 4Å: Chain A: R.58, H.61, H.100, D.101, D.205 Ligands: MG.2, XG4.5 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.61, A:H.100, A:D.101, A:D.205, A:D.205 FE.9: 7 residues within 4Å: Chain B: R.58, H.61, H.100, D.101, D.205 Ligands: MG.10, XG4.13 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.61, B:H.100, B:D.101, B:D.205, B:D.205 FE.18: 7 residues within 4Å: Chain C: R.58, H.61, H.100, D.101, D.205 Ligands: MG.19, XG4.22 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:H.61, C:H.100, C:D.101, C:D.205, C:D.205 FE.26: 7 residues within 4Å: Chain D: R.58, H.61, H.100, D.101, D.205 Ligands: MG.27, XG4.30 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.61, D:H.100, D:D.101, D:D.205

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

MG.2: 6 residues within 4Å: Chain A: H.100, D.101, H.127, D.205 Ligands: FE.1, XG4.5 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: XG4.5 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain A: K.10 Ligands: CZF.6, XG4.17 No protein-ligand interaction detected (PLIP) MG.10: 6 residues within 4Å: Chain B: H.100, D.101, H.127, D.205 Ligands: FE.9, XG4.13 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.101, B:H.127 MG.11: 3 residues within 4Å: Chain B: D.203, K.206 Ligands: XG4.13 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain B: K.10 Ligands: CZF.14, XG4.25 No protein-ligand interaction detected (PLIP) MG.19: 6 residues within 4Å: Chain C: H.100, D.101, H.127, D.205 Ligands: FE.18, XG4.22 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.101, C:H.127 MG.20: 3 residues within 4Å: Chain C: D.203, K.206 Ligands: XG4.22 No protein-ligand interaction detected (PLIP) MG.21: 2 residues within 4Å: Ligands: XG4.8, CZF.23 No protein-ligand interaction detected (PLIP) MG.27: 6 residues within 4Å: Chain D: H.100, D.101, H.127, D.205 Ligands: FE.26, XG4.30 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.101, D:H.127 MG.28: 3 residues within 4Å: Chain D: D.203, K.206 Ligands: XG4.30 No protein-ligand interaction detected (PLIP) MG.29: 3 residues within 4Å: Chain D: K.10 Ligands: XG4.16, CZF.31 No protein-ligand interaction detected (PLIP)

8 x XG4: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]guanosine(Non-covalent)

XG4.5: 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 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:L.44, A:Y.268 Hydrogen bonds: A:Q.43, A:L.44, A:R.58, A:R.58, A:Y.209, A:D.213, A:Y.268 Salt bridges: A:K.206, A:R.260, A:D.277 pi-Stacking: A:H.109 XG4.8: 21 residues within 4Å: Chain A: D.224, 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, P.52, G.218, I.219, R.266, H.270, K.271, V.272 Ligands: MG.21, CZF.23 17 PLIP interactions: 9 interactions with chain A, 6 interactions with chain D, 2 interactions with chain C Hydrogen bonds: A:R.227, A:R.227, A:K.248, A:N.252, D:V.50, D:G.218, D:K.271, C:N.13, C:N.13 Salt bridges: A:R.246, A:K.248, A:K.417, D:K.271 pi-Cation interactions: A:R.227, A:R.227 Hydrophobic interactions: D:V.50, D:F.51 XG4.13: 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, MG.10, MG.11 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.44, B:Y.268 Hydrogen bonds: B:Q.43, B:L.44, B:R.58, B:R.58, B:D.101, B:Y.209, B:D.213, B:Y.268, B:Q.269 Salt bridges: B:K.206, B:R.260, B:D.277 XG4.16: 19 residues within 4Å: Chain B: D.224, R.227, R.246, K.248, N.252, K.417 Chain C: V.50, F.51, G.218, I.219, R.266, H.270, K.271 Chain D: V.11, I.12, N.13, H.19 Ligands: MG.29, CZF.31 18 PLIP interactions: 7 interactions with chain C, 9 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: C:V.50, C:F.51 Hydrogen bonds: C:V.50, C:G.218, C:H.270, C:K.271, B:R.227, B:R.227, B:N.252, D:N.13, D:N.13 Salt bridges: C:K.271, B:D.224, B:R.246, B:K.248, B:K.417 pi-Cation interactions: B:R.227, B:R.227 XG4.17: 20 residues within 4Å: Chain A: V.11, I.12, N.13, H.19 Chain B: V.50, F.51, G.218, I.219, R.266, H.270, K.271, V.272 Chain C: D.224, R.227, R.246, K.248, N.252, K.417 Ligands: MG.4, CZF.6 18 PLIP interactions: 7 interactions with chain B, 9 interactions with chain C, 2 interactions with chain A Hydrophobic interactions: B:V.50, B:F.51 Hydrogen bonds: B:V.50, B:G.218, B:H.270, B:K.271, C:R.227, C:R.227, C:K.248, C:N.252, A:N.13, A:N.13 Salt bridges: B:K.271, C:R.246, C:K.248, C:K.417 pi-Cation interactions: C:R.227, C:R.227 XG4.22: 20 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.18, MG.19, MG.20 11 PLIP interactions: 11 interactions with chain C Hydrophobic interactions: C:L.44, C:Y.268 Hydrogen bonds: C:Q.43, C:L.44, C:R.58, C:R.58, C:D.213, C:Q.269 Salt bridges: C:K.206, C:R.260, C:D.277 XG4.25: 20 residues within 4Å: Chain A: V.50, F.51, G.218, I.219, R.266, H.270, K.271, V.272 Chain B: V.11, I.12, N.13, H.19 Chain D: D.224, R.227, R.246, K.248, N.252, K.417 Ligands: MG.12, CZF.14 19 PLIP interactions: 10 interactions with chain D, 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: D:D.224, D:R.227, D:R.227, D:K.248, D:N.252, A:V.50, A:G.218, A:H.270, A:K.271, B:N.13, B:N.13 Salt bridges: D:R.246, D:K.248, D:K.417, A:K.271 pi-Cation interactions: D:R.227, D:R.227 Hydrophobic interactions: A:V.50, A:F.51 XG4.30: 20 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, D.277 Ligands: FE.26, MG.27, MG.28 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:Y.268 Hydrogen bonds: D:Q.43, D:L.44, D:R.58, D:R.58, D:D.101, D:Y.209, D:Y.209, D:D.213, D:Q.269 Salt bridges: D:K.206, D:R.260, D:D.277 pi-Stacking: D:Y.268 pi-Cation interactions: 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: 16 residues within 4Å: Chain A: K.10, V.11, I.12, 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, XG4.17 16 PLIP interactions: 9 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, A:K.10, B:K.271, B:R.345, B:K.349, C:K.417, C:K.417 pi-Cation interactions: B:R.345 CZF.14: 14 residues within 4Å: Chain A: Y.49, V.50, V.272, R.345 Chain B: K.10, V.11, I.12, N.31, Q.36, R.39, F.59 Chain D: K.417 Ligands: MG.12, XG4.25 17 PLIP interactions: 6 interactions with chain A, 2 interactions with chain D, 9 interactions with chain B Hydrogen bonds: 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, A:K.349, D:K.417, D:K.417, B:K.10, B:K.10 pi-Cation interactions: A:R.345 CZF.23: 16 residues within 4Å: Chain A: K.417 Chain C: K.10, V.11, I.12, I.30, N.31, Q.36, R.39, F.59 Chain D: Y.49, V.50, V.272, R.345, K.349 Ligands: XG4.8, MG.21 16 PLIP interactions: 6 interactions with chain D, 2 interactions with chain A, 8 interactions with chain C Hydrogen bonds: D:R.345, C:K.10, C:K.10, C:N.31, C:N.31, C:Q.36, C:R.39 Salt bridges: D:K.271, D:R.345, D:K.349, D:K.349, A:K.417, A:K.417, C:K.10, C:K.10 pi-Cation interactions: D:R.345 CZF.31: 15 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, N.31, Q.36, R.39, F.59 Ligands: XG4.16, MG.29 16 PLIP interactions: 9 interactions with chain D, 2 interactions with chain B, 5 interactions with chain C Hydrogen bonds: D:K.10, D:K.10, D:V.11, D:N.31, D:N.31, D:Q.36, D:R.39, C:R.345 Salt bridges: D:K.10, D:K.10, B:K.417, B:K.417, C:K.271, C:R.345, 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 4 PLIP interactions: 4 interactions with chain A Salt bridges: A:R.199, A:R.242, A:H.411, A:R.425 SO4.15: 3 residues within 4Å: Chain B: R.199, R.242, H.411 3 PLIP interactions: 3 interactions with chain B Salt bridges: B:R.199, B:R.242, B:H.411 SO4.24: 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

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
M

B
N

C
O

D
P

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

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