SMTL ID : 6txf.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 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: MN.2, DZ4.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.61, A:H.100, A:D.101, A:D.205, H2O.1 FE.9: 7 residues within 4Å: Chain B: R.58, H.61, H.100, D.101, D.205 Ligands: MN.10, DZ4.13 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.61, B:H.100, B:D.101, B:D.205, H2O.3 FE.15: 7 residues within 4Å: Chain C: R.58, H.61, H.100, D.101, D.205 Ligands: MN.16, DZ4.19 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.61, C:H.100, C:D.101, C:D.205, H2O.4 FE.23: 7 residues within 4Å: Chain D: R.58, H.61, H.100, D.101, D.205 Ligands: MN.24, DZ4.27 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.61, D:H.100, D:D.101, D:D.205, H2O.7

12 x MN: MANGANESE (II) ION(Non-covalent)(Non-functional Binders)

MN.2: 6 residues within 4Å: Chain A: H.100, D.101, H.104, H.127 Ligands: FE.1, DZ4.5 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.101, A:H.127, H2O.1, H2O.1, H2O.1 MN.3: 1 residues within 4Å: Ligands: DZ4.5 No protein-ligand interaction detected (PLIP) MN.4: 3 residues within 4Å: Chain C: K.417 Ligands: CZF.6, DZ4.8 No protein-ligand interaction detected (PLIP) MN.10: 6 residues within 4Å: Chain B: H.100, D.101, H.104, H.127 Ligands: FE.9, DZ4.13 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.101, B:H.127, H2O.2, H2O.3, H2O.3 MN.11: 2 residues within 4Å: Chain B: K.206 Ligands: DZ4.13 No protein-ligand interaction detected (PLIP) MN.12: 3 residues within 4Å: Chain D: K.417 Ligands: DZ4.7, CZF.14 No protein-ligand interaction detected (PLIP) MN.16: 6 residues within 4Å: Chain C: H.100, D.101, H.104, H.127 Ligands: FE.15, DZ4.19 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.101, C:H.127, H2O.4, H2O.5, H2O.5 MN.17: 1 residues within 4Å: Ligands: DZ4.19 No protein-ligand interaction detected (PLIP) MN.18: 3 residues within 4Å: Chain A: K.417 Ligands: CZF.20, DZ4.22 No protein-ligand interaction detected (PLIP) MN.24: 6 residues within 4Å: Chain D: H.100, D.101, H.104, H.127 Ligands: FE.23, DZ4.27 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.101, D:H.127, H2O.6, H2O.6, H2O.7 MN.25: 2 residues within 4Å: Chain D: K.206 Ligands: DZ4.27 No protein-ligand interaction detected (PLIP) MN.26: 3 residues within 4Å: Chain B: K.417 Ligands: DZ4.21, CZF.28 No protein-ligand interaction detected (PLIP)

8 x DZ4: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine(Non-covalent)

DZ4.5: 20 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, Y.268, Q.269, N.274, D.277 Ligands: FE.1, MN.2, MN.3 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:L.44, A:Y.268 Hydrogen bonds: A:Q.43, A:R.58, A:R.58, A:Y.209, A:D.213, A:Q.269, A:Q.269, A:N.274 Water bridges: A:E.128, A:E.128, A:E.128, A:K.206 Salt bridges: A:K.206, A:R.260 DZ4.7: 17 residues within 4Å: Chain A: V.50, F.51, I.219, R.266, H.270, K.271 Chain B: V.11, I.12, N.13, H.19 Chain D: R.227, R.246, K.248, N.252, K.417 Ligands: MN.12, CZF.14 18 PLIP interactions: 9 interactions with chain D, 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: D:R.227, D:R.227, D:N.252, D:N.252, A:V.50, A:H.270, A:K.271, 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 DZ4.8: 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: MN.4, CZF.6 21 PLIP interactions: 12 interactions with chain C, 2 interactions with chain A, 7 interactions with chain B Hydrogen bonds: C:R.227, C:R.227, C:N.252, C:N.252, A:N.13, A:N.13, B:V.50, B:H.270, B:K.271, B:K.271 Water bridges: C:R.246, C:K.417, C:K.417 Salt bridges: C:R.246, C:K.248, C:K.417, B:K.271 pi-Cation interactions: C:R.227, C:R.227 Hydrophobic interactions: B:V.50, B:F.51 DZ4.13: 20 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, Y.268, Q.269, N.274, D.277 Ligands: FE.9, MN.10, MN.11 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:L.44, B:Y.268 Hydrogen bonds: B:Q.43, B:R.58, B:R.58, B:Y.209, B:D.213, B:Q.269, B:Q.269, B:N.274 Water bridges: B:G.46, B:E.128, B:E.128, B:E.128 Salt bridges: B:K.206, B:R.260 DZ4.19: 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, Y.268, Q.269, N.274, D.277 Ligands: FE.15, MN.16, MN.17 14 PLIP interactions: 14 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.213, C:Q.269, C:Q.269, C:N.274 Water bridges: C:E.128, C:E.128, C:K.206 Salt bridges: C:K.206, C:R.260 DZ4.21: 17 residues within 4Å: Chain B: R.227, R.246, K.248, N.252, K.417 Chain C: V.50, F.51, I.219, R.266, H.270, K.271 Chain D: V.11, I.12, N.13, H.19 Ligands: MN.26, CZF.28 18 PLIP interactions: 9 interactions with chain B, 7 interactions with chain C, 2 interactions with chain D Hydrogen bonds: B:R.227, B:R.227, B:N.252, B:N.252, C:V.50, C:H.270, C:K.271, C:K.271, D:N.13, D:N.13 Salt bridges: B:R.246, B:K.248, B:K.417, C:K.271 pi-Cation interactions: B:R.227, B:R.227 Hydrophobic interactions: C:V.50, C:F.51 DZ4.22: 19 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, V.272 Ligands: MN.18, CZF.20 21 PLIP interactions: 7 interactions with chain D, 12 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: D:V.50, D:F.51 Hydrogen bonds: D:V.50, D:H.270, D:K.271, D:K.271, A:R.227, A:R.227, A:N.252, A:N.252, C:N.13, C:N.13 Salt bridges: D:K.271, A:R.246, A:K.248, A:K.417 Water bridges: A:R.246, A:K.417, A:K.417 pi-Cation interactions: A:R.227, A:R.227 DZ4.27: 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, Y.268, Q.269, N.274, D.277 Ligands: FE.23, MN.24, MN.25 14 PLIP interactions: 14 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.213, D:Q.269, D:Q.269, D:N.274 Water bridges: D:G.46, D:E.128, D:E.128 Salt bridges: D:K.206, D:R.260

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: 15 residues within 4Å: Chain A: K.10, V.11, I.12, 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: MN.4, DZ4.8 19 PLIP interactions: 6 interactions with chain B, 9 interactions with chain A, 4 interactions with chain C Hydrogen bonds: B:R.345, A:K.10, A:K.10, A:V.11, A:N.31, A:N.31, A:Q.36, A:R.39 Salt bridges: B:R.345, B:K.349, B:K.349, A:K.10, A:K.10, C:K.417, C:K.417 pi-Cation interactions: B:R.345, B:R.345 Water bridges: C:K.417, C:K.417 CZF.14: 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, N.31, Q.36, R.39, F.59 Chain D: K.417 Ligands: DZ4.7, MN.12 16 PLIP interactions: 9 interactions with chain B, 5 interactions with chain A, 2 interactions with chain D Hydrogen bonds: B:K.10, B:K.10, B:V.11, B:N.31, B:N.31, B:Q.36, B:R.39, A:R.345 Salt bridges: B:K.10, B:K.10, A:R.345, A:K.349, A:K.349, D:K.417, D:K.417 pi-Cation interactions: A:R.345 CZF.20: 15 residues within 4Å: Chain A: K.417 Chain C: K.10, V.11, I.12, N.31, Q.36, R.39, F.59 Chain D: Y.49, V.50, V.272, R.345, K.349 Ligands: MN.18, DZ4.22 20 PLIP interactions: 9 interactions with chain C, 7 interactions with chain D, 4 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, D:R.345 Salt bridges: C:K.10, C:K.10, D:R.345, D:K.349, D:K.349, A:K.417, A:K.417 pi-Cation interactions: D:R.345, D:R.345 Water bridges: A:K.417, A:K.417 CZF.28: 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, N.31, Q.36, R.39, F.59 Ligands: DZ4.21, MN.26 16 PLIP interactions: 5 interactions with chain C, 9 interactions with chain D, 2 interactions with chain B Hydrogen bonds: C:R.345, D:K.10, D:K.10, D:V.11, D:N.31, D:N.31, D:Q.36, D:R.39 Salt bridges: C:R.345, C:K.349, C:K.349, D:K.10, D:K.10, B:K.417, B:K.417 pi-Cation interactions: C:R.345

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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