SMTL ID : 4bzb.1

Crystal structure of the tetrameric dGTP-bound SAMHD1 mutant catalytic core

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-tetramer

Ligands

12 x DGT: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE(Non-covalent)

DGT.1: 16 residues within 4Å: Chain A: Q.73, L.74, R.88, R.130, H.134, H.139, H.157, D.235, K.236, Y.239, D.243, R.290, H.294, Y.298, Q.299 Ligands: MG.2 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:L.74, A:Y.298 Hydrogen bonds: A:Q.73, A:L.74, A:R.88, A:Y.298, A:Q.299 Water bridges: A:G.76, A:R.130, A:R.130, A:R.130, A:R.130, A:R.130, A:R.130, A:K.236, A:R.290, A:R.290, A:R.290, A:G.432 Salt bridges: A:R.88, A:R.130, A:H.134, A:H.157, A:H.157, A:K.236, A:R.290, A:D.307 DGT.3: 20 residues within 4Å: Chain A: V.80, F.81, I.249, R.296, H.300, K.301, V.302 Chain C: D.254, R.257, F.261, R.276, K.278, N.282, K.447 Chain D: V.41, I.42, N.43, H.49 Ligands: MG.4, DGT.5 25 PLIP interactions: 15 interactions with chain C, 8 interactions with chain A, 2 interactions with chain D Hydrogen bonds: C:R.257, C:N.282, D:N.43, D:N.43 Water bridges: C:D.254, C:R.257, C:R.257, C:N.282, A:R.296 Salt bridges: C:D.254, C:R.257, C:R.276, C:K.278, C:K.278, C:K.278, C:K.447, A:H.300, A:H.300, A:K.301, A:K.301, A:K.301 pi-Cation interactions: C:R.257, C:R.257 Hydrophobic interactions: A:V.80, A:F.81 DGT.5: 16 residues within 4Å: Chain A: Y.79, V.80, V.302, R.375, K.379 Chain C: K.447 Chain D: K.40, V.41, I.42, I.60, D.61, Q.66, R.69, F.89 Ligands: DGT.3, MG.4 21 PLIP interactions: 13 interactions with chain D, 6 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: D:I.42 Hydrogen bonds: D:Q.66, D:R.69, A:R.375 Water bridges: D:K.40, D:K.40, D:K.40, D:K.40, D:K.40, D:D.61, A:K.379 Salt bridges: D:K.40, D:K.40, D:K.40, D:D.61, A:R.375, A:K.379, A:K.379, C:K.447, C:K.447 pi-Cation interactions: A:R.375 DGT.6: 16 residues within 4Å: Chain B: Q.73, L.74, R.88, R.130, H.134, H.139, H.157, D.235, K.236, Y.239, D.243, R.290, H.294, Y.298, Q.299 Ligands: MG.7 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:L.74, B:Y.298 Hydrogen bonds: B:Q.73, B:L.74, B:R.88, B:N.131, B:D.235, B:Y.239, B:Y.298, B:Q.299 Water bridges: B:G.76, B:R.88, B:R.88, B:R.88, B:R.130, B:R.130, B:R.130, B:R.130, B:E.158, B:R.290, B:R.290 Salt bridges: B:R.88, B:R.130, B:H.134, B:H.157, B:H.157, B:K.236, B:R.290 DGT.8: 20 residues within 4Å: Chain B: V.80, F.81, I.249, R.296, H.300, K.301, V.302 Chain C: V.41, I.42, N.43, H.49 Chain D: D.254, R.257, F.261, R.276, K.278, N.282, K.447 Ligands: MG.9, DGT.10 26 PLIP interactions: 16 interactions with chain D, 8 interactions with chain B, 2 interactions with chain C Hydrogen bonds: D:R.257, D:N.282, C:N.43, C:N.43 Water bridges: D:R.257, D:K.278, D:N.282, D:K.447, D:K.447, B:R.296 Salt bridges: D:D.254, D:R.257, D:R.276, D:K.278, D:K.278, D:K.278, D:K.447, B:H.300, B:H.300, B:K.301, B:K.301, B:K.301 pi-Cation interactions: D:R.257, D:R.257 Hydrophobic interactions: B:V.80, B:F.81 DGT.10: 16 residues within 4Å: Chain B: Y.79, V.80, V.302, R.375, K.379 Chain C: K.40, V.41, I.42, I.60, D.61, Q.66, R.69, F.89 Chain D: K.447 Ligands: DGT.8, MG.9 25 PLIP interactions: 8 interactions with chain B, 12 interactions with chain C, 5 interactions with chain D Hydrogen bonds: B:R.375, C:Q.66, C:R.69 Water bridges: B:K.379, B:K.379, B:K.379, C:K.40, C:K.40, C:K.40, C:K.40, C:K.40, D:K.447, D:K.447, D:K.447 Salt bridges: B:R.375, B:K.379, B:K.379, C:K.40, C:K.40, C:K.40, C:D.61, D:K.447, D:K.447 pi-Cation interactions: B:R.375 Hydrophobic interactions: C:I.42 DGT.11: 17 residues within 4Å: Chain C: Q.73, L.74, R.88, R.130, N.131, H.134, H.139, H.157, D.235, K.236, Y.239, D.243, R.290, H.294, Y.298, Q.299 Ligands: MG.12 26 PLIP interactions: 26 interactions with chain C Hydrophobic interactions: C:L.74, C:Y.298 Hydrogen bonds: C:Q.73, C:L.74, C:R.88, C:N.131, C:D.235, C:Y.239, C:Y.298, C:Q.299 Water bridges: C:R.130, C:R.130, C:R.130, C:R.130, C:R.130, C:H.139, C:E.158, C:R.290, C:R.290 Salt bridges: C:R.88, C:R.130, C:H.134, C:H.157, C:H.157, C:K.236, C:R.290 DGT.13: 20 residues within 4Å: Chain A: D.254, R.257, F.261, R.276, K.278, N.282, K.447 Chain B: V.41, I.42, N.43, H.49 Chain C: V.80, F.81, I.249, R.296, H.300, K.301, V.302 Ligands: MG.14, DGT.15 25 PLIP interactions: 15 interactions with chain A, 2 interactions with chain B, 8 interactions with chain C Hydrogen bonds: A:R.257, A:N.282, B:N.43, B:N.43 Water bridges: A:R.257, A:K.278, A:N.282, A:K.447, C:R.296 Salt bridges: A:D.254, A:R.257, A:R.276, A:K.278, A:K.278, A:K.278, A:K.447, C:H.300, C:H.300, C:K.301, C:K.301, C:K.301 pi-Cation interactions: A:R.257, A:R.257 Hydrophobic interactions: C:V.80, C:F.81 DGT.15: 16 residues within 4Å: Chain A: K.447 Chain B: K.40, V.41, I.42, I.60, D.61, Q.66, R.69, F.89 Chain C: Y.79, V.80, V.302, R.375, K.379 Ligands: DGT.13, MG.14 24 PLIP interactions: 2 interactions with chain A, 14 interactions with chain B, 8 interactions with chain C Salt bridges: A:K.447, A:K.447, B:K.40, B:K.40, B:K.40, B:D.61, C:R.375, C:K.379, C:K.379 Hydrophobic interactions: B:I.42 Hydrogen bonds: B:Q.66, B:R.69, C:R.375 Water bridges: B:K.40, B:K.40, B:K.40, B:K.40, B:K.40, B:D.61, B:Q.66, C:K.379, C:K.379, C:Y.380 pi-Cation interactions: C:R.375 DGT.16: 17 residues within 4Å: Chain D: Q.73, L.74, R.88, R.130, N.131, H.134, H.139, H.157, D.235, K.236, Y.239, D.243, R.290, H.294, Y.298, Q.299 Ligands: MG.17 26 PLIP interactions: 26 interactions with chain D Hydrophobic interactions: D:L.74, D:Y.298 Hydrogen bonds: D:Q.73, D:L.74, D:R.88, D:N.131, D:Y.298, D:Q.299 Water bridges: D:R.88, D:R.88, D:R.88, D:R.130, D:R.130, D:R.130, D:H.139, D:R.144, D:R.290, D:R.290, D:R.290 Salt bridges: D:R.88, D:R.130, D:H.134, D:H.157, D:H.157, D:K.236, D:R.290 DGT.18: 20 residues within 4Å: Chain A: V.41, I.42, N.43, H.49 Chain B: D.254, R.257, F.261, R.276, K.278, N.282, K.447 Chain D: V.80, F.81, I.249, R.296, H.300, K.301, V.302 Ligands: MG.19, DGT.20 27 PLIP interactions: 17 interactions with chain B, 2 interactions with chain A, 8 interactions with chain D Hydrogen bonds: B:R.257, B:N.282, A:N.43, A:N.43 Water bridges: B:D.254, B:R.257, B:K.278, B:N.282, B:K.447, B:K.447, D:R.296 Salt bridges: B:D.254, B:R.257, B:R.276, B:K.278, B:K.278, B:K.278, B:K.447, D:H.300, D:H.300, D:K.301, D:K.301, D:K.301 pi-Cation interactions: B:R.257, B:R.257 Hydrophobic interactions: D:V.80, D:F.81 DGT.20: 16 residues within 4Å: Chain A: K.40, V.41, I.42, I.60, D.61, Q.66, R.69, F.89 Chain B: K.447 Chain D: Y.79, V.80, V.302, R.375, K.379 Ligands: DGT.18, MG.19 27 PLIP interactions: 14 interactions with chain A, 8 interactions with chain D, 5 interactions with chain B Hydrophobic interactions: A:I.42 Hydrogen bonds: A:Q.66, A:R.69, D:R.375 Water bridges: A:T.38, A:K.40, A:K.40, A:K.40, A:K.40, A:K.40, A:D.61, D:K.379, D:K.379, D:Y.380, B:K.447, B:K.447, B:K.447 Salt bridges: A:K.40, A:K.40, A:K.40, A:D.61, D:R.375, D:K.379, D:K.379, B:K.447, B:K.447 pi-Cation interactions: D:R.375

8 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 3 residues within 4Å: Chain A: D.233, K.236 Ligands: DGT.1 No protein-ligand interaction detected (PLIP) MG.4: 4 residues within 4Å: Chain C: K.447 Chain D: K.40 Ligands: DGT.3, DGT.5 No protein-ligand interaction detected (PLIP) MG.7: 3 residues within 4Å: Chain B: R.130, K.236 Ligands: DGT.6 No protein-ligand interaction detected (PLIP) MG.9: 4 residues within 4Å: Chain C: K.40 Chain D: K.447 Ligands: DGT.8, DGT.10 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain C: D.233, K.236 Ligands: DGT.11 No protein-ligand interaction detected (PLIP) MG.14: 3 residues within 4Å: Chain B: K.40 Ligands: DGT.13, DGT.15 No protein-ligand interaction detected (PLIP) MG.17: 2 residues within 4Å: Chain D: K.236 Ligands: DGT.16 No protein-ligand interaction detected (PLIP) MG.19: 3 residues within 4Å: Chain A: K.40 Ligands: DGT.18, DGT.20 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ji, X. et al., Mechanism of Allosteric Activation of Samhd1 by Dgtp. Nat.Struct.Mol.Biol. (2013)

Release Date

2013-10-23

Peptides

DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1

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