SMTL ID : 6xu1.2 (1 other biounit)

Crystal structure of tetrameric human H215A-SAMHD1 (residues 109-626) with GTP, dAMPNPP and Mg

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 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, 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.2 FE.9: 7 residues within 4Å: Chain B: R.58, H.61, H.100, D.101, D.205 Ligands: MG.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.6 FE.16: 7 residues within 4Å: Chain C: R.58, H.61, H.100, D.101, D.205 Ligands: MG.17, DZ4.20 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.10 FE.23: 7 residues within 4Å: Chain D: R.58, H.61, H.100, D.101, D.205 Ligands: MG.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.14

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

MG.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.2, H2O.2 MG.3: 2 residues within 4Å: Chain A: K.206 Ligands: DZ4.5 No protein-ligand interaction detected (PLIP) MG.4: 3 residues within 4Å: Chain A: K.10 Ligands: GTP.6, DZ4.15 No protein-ligand interaction detected (PLIP) MG.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.5, H2O.5, H2O.6 MG.11: 3 residues within 4Å: Chain B: D.203, K.206 Ligands: DZ4.13 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain B: K.10 Ligands: GTP.7, DZ4.22 No protein-ligand interaction detected (PLIP) MG.17: 6 residues within 4Å: Chain C: H.100, D.101, H.104, H.127 Ligands: FE.16, DZ4.20 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.101, C:H.127, H2O.10, H2O.10, H2O.11 MG.18: 2 residues within 4Å: Chain C: K.206 Ligands: DZ4.20 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain C: K.10 Ligands: DZ4.8, GTP.21 No protein-ligand interaction detected (PLIP) MG.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.14, H2O.14, H2O.14 MG.25: 1 residues within 4Å: Ligands: DZ4.27 No protein-ligand interaction detected (PLIP) MG.26: 3 residues within 4Å: Chain D: K.10 Ligands: DZ4.14, GTP.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, A.109, H.127, D.205, K.206, Y.209, D.213, R.260, Y.268, Q.269, N.274, D.277 Ligands: FE.1, MG.2, MG.3 15 PLIP interactions: 15 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.101, A:D.213, A:Q.269, A:Q.269, A:N.274 Water bridges: A:A.109, A:H.127, A:E.128 Salt bridges: A:K.206, A:R.260 DZ4.8: 18 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, I.219, R.266, H.270, K.271, V.272 Ligands: MG.19, GTP.21 18 PLIP interactions: 9 interactions with chain A, 7 interactions with chain D, 2 interactions with chain C Hydrogen bonds: A:R.227, A:R.227, A:N.252, A:N.252, D:V.50, D:H.270, D:K.271, 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 DZ4.13: 20 residues within 4Å: Chain B: Q.43, L.44, R.58, H.61, D.101, H.104, A.109, H.127, D.205, K.206, Y.209, D.213, R.260, Y.268, Q.269, N.274, D.277 Ligands: FE.9, MG.10, MG.11 19 PLIP interactions: 19 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.101, B:Y.209, B:D.213, B:Q.269, B:Q.269, B:N.274 Water bridges: B:G.46, B:A.109, B:R.114, B:E.128, B:E.128, B:E.128 Salt bridges: B:K.206, B:R.260 DZ4.14: 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.26, GTP.28 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:H.270, C:K.271, C:K.271, B:R.227, B:R.227, B:N.252, B:N.252, D:N.13, D:N.13 Salt bridges: C:K.271, B:R.246, B:K.248, B:K.417 pi-Cation interactions: B:R.227, B:R.227 DZ4.15: 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 18 PLIP interactions: 9 interactions with chain C, 7 interactions with chain B, 2 interactions with chain A Hydrogen bonds: C:R.227, C:R.227, C:N.252, C:N.252, B:V.50, B:H.270, B:K.271, B:K.271, A:N.13, A:N.13 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 DZ4.20: 20 residues within 4Å: Chain C: Q.43, L.44, R.58, H.61, D.101, H.104, A.109, H.127, D.205, K.206, Y.209, D.213, R.260, Y.268, Q.269, N.274, D.277 Ligands: FE.16, MG.17, MG.18 17 PLIP interactions: 17 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.101, C:Y.209, C:D.213, C:Q.269, C:Q.269, C:N.274 Water bridges: C:A.109, C:E.128, C:E.128, C:E.128 Salt bridges: C:K.206, C:R.260 DZ4.22: 16 residues within 4Å: Chain A: V.50, F.51, 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: GTP.7, MG.12 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 DZ4.27: 21 residues within 4Å: Chain D: Q.43, L.44, R.58, H.61, D.101, H.104, A.109, H.127, D.205, K.206, Y.209, D.213, R.260, H.264, Y.268, Q.269, N.274, D.277 Ligands: FE.23, MG.24, MG.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.101, D:D.213, D:Q.269, D:Q.269, D:N.274 Water bridges: D:A.109, D:E.128 Salt bridges: D:K.206, D:R.260

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

GTP.6: 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.4, DZ4.15 14 PLIP interactions: 8 interactions with chain A, 2 interactions with chain C, 4 interactions with chain B Hydrogen bonds: A:V.11, A:Q.36, A:R.39 Water bridges: A:K.10 Salt bridges: A:K.10, A:K.10, A:K.10, A:D.31, C:K.417, C:K.417, B:R.345, B:K.349, B:K.349 pi-Cation interactions: B:R.345 GTP.7: 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.12, DZ4.22 15 PLIP interactions: 5 interactions with chain A, 8 interactions with chain B, 2 interactions with chain D Hydrogen bonds: A:R.345, B:V.11, B:Q.36, B:R.39 Salt bridges: A:R.345, A:K.349, A:K.349, B:K.10, B:K.10, B:K.10, B:D.31, D:K.417, D:K.417 pi-Cation interactions: A:R.345 Water bridges: B:K.10 GTP.21: 16 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, K.349 Ligands: DZ4.8, MG.19 15 PLIP interactions: 5 interactions with chain D, 8 interactions with chain C, 2 interactions with chain A Hydrogen bonds: D:R.345, C:V.11, C:Q.36, C:R.39 Salt bridges: D:R.345, D:K.349, D:K.349, C:K.10, C:K.10, C:K.10, C:D.31, A:K.417, A:K.417 pi-Cation interactions: D:R.345 Water bridges: C:K.10 GTP.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, D.31, Q.36, R.39, F.59 Ligands: DZ4.14, MG.26 16 PLIP interactions: 9 interactions with chain D, 5 interactions with chain C, 2 interactions with chain B Hydrogen bonds: D:V.11, D:Q.36, D:R.39, C:R.345 Water bridges: D:K.10, D:D.31 Salt bridges: D:K.10, D:K.10, D:K.10, D:D.31, C:R.345, C:K.349, C:K.349, 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
E

B
F

C
G

D
H

Deoxynucleoside triphosphate triphosphohydrolase SAMHD1

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