SMTL ID : 4bzc.1

Crystal structure of the tetrameric dGTP-bound wild type SAMHD1 catalytic core

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.88 Å

Oligo State

homo-tetramer

Ligands

12 x T8T: 2'-deoxyguanosine-5'-O-(1-thiotriphosphate)(Non-covalent)(Covalent)

T8T.1: 17 residues within 4Å: Chain A: Q.73, L.74, R.88, D.131, H.134, H.139, H.157, E.158, D.235, K.236, Y.239, D.243, R.290, H.294, Y.298, Q.299 Ligands: MN.2 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:L.74, A:Y.298 Hydrogen bonds: A:Q.73, A:L.74, A:R.88, A:R.88, A:E.158, A:D.243, A:Q.299 Salt bridges: A:H.157, A:K.236, A:R.290 T8T.3: 19 residues within 4Å: Chain A: V.80, F.81, G.248, I.249, R.296, H.300, K.301 Chain C: R.257, F.261, R.276, K.278, N.282, K.447 Chain D: V.41, I.42, N.43, H.49 Ligands: T8T.4, MG.5 18 PLIP interactions: 7 interactions with chain A, 2 interactions with chain D, 9 interactions with chain C Hydrophobic interactions: A:V.80, A:F.81 Hydrogen bonds: A:V.80, A:R.296, D:N.43, D:N.43, C:R.257, C:R.257, C:N.282 Salt bridges: A:H.300, A:K.301, A:K.301, C:R.276, C:K.278, C:K.278, C:K.447 pi-Cation interactions: C:R.257, C:R.257 T8T.4: 18 residues within 4Å: Chain A: Y.79, V.80, K.301, V.302, R.375, K.379 Chain C: K.447 Chain D: K.40, V.41, I.42, V.57, I.60, D.61, Q.66, R.69, F.89 Ligands: T8T.3, MG.5 17 PLIP interactions: 6 interactions with chain A, 9 interactions with chain D, 2 interactions with chain C Hydrogen bonds: A:R.375, A:R.375, D:V.41, D:Q.66, D:R.69 Salt bridges: A:K.301, A:K.379, A:K.379, D:K.40, D:K.40, D:D.61, C:K.447, C:K.447 pi-Cation interactions: A:R.375 Hydrophobic interactions: D:I.42 Water bridges: D:K.40, D:K.40 T8T.6: 16 residues within 4Å: Chain B: Q.73, L.74, R.88, D.131, H.134, H.139, H.157, D.235, K.236, Y.239, D.243, R.290, H.294, Y.298, Q.299 Ligands: MN.7 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.74, B:Y.298 Hydrogen bonds: B:Q.73, B:L.74, B:R.88, B:R.88, B:H.139, B:D.235, B:Y.239, B:D.243, B:Q.299 Salt bridges: B:H.157, B:K.236, B:R.290 pi-Stacking: B:Y.298 T8T.8: 19 residues within 4Å: Chain B: V.80, F.81, G.248, I.249, R.296, H.300, K.301 Chain C: V.41, I.42, N.43 Chain D: F.253, R.257, F.261, R.276, K.278, N.282, K.447 Ligands: T8T.9, MG.10 19 PLIP interactions: 11 interactions with chain D, 6 interactions with chain B, 2 interactions with chain C Hydrogen bonds: D:R.257, D:R.257, D:N.282, B:V.80, C:N.43, C:N.43 Water bridges: D:K.447, D:K.447 Salt bridges: D:R.276, D:K.278, D:K.278, D:K.447, B:H.300, B:K.301, B:K.301 pi-Cation interactions: D:R.257, D:R.257 Hydrophobic interactions: B:V.80, B:F.81 T8T.9: 18 residues within 4Å: Chain B: Y.79, V.80, K.301, V.302, R.375, K.379 Chain C: K.40, V.41, I.42, V.57, I.60, D.61, Q.66, R.69, F.89 Chain D: K.447 Ligands: T8T.8, MG.10 18 PLIP interactions: 7 interactions with chain C, 4 interactions with chain D, 7 interactions with chain B Hydrophobic interactions: C:I.42 Hydrogen bonds: C:V.41, C:Q.66, C:R.69, B:R.375, B:R.375 Salt bridges: C:K.40, C:K.40, C:D.61, D:K.447, D:K.447, B:K.301, B:K.379, B:K.379 Water bridges: D:K.447, D:K.447 pi-Cation interactions: B:R.375, B:R.375 T8T.11: 17 residues within 4Å: Chain C: Q.73, L.74, R.88, D.131, H.134, H.139, H.157, E.158, D.235, K.236, Y.239, D.243, R.290, H.294, Y.298, Q.299 Ligands: MN.12 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:L.74, C:Y.298 Hydrogen bonds: C:Q.73, C:L.74, C:R.88, C:R.88, C:Y.239, C:D.243, C:Q.299 Salt bridges: C:H.157, C:K.236, C:R.290 T8T.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 Chain C: V.80, F.81, G.248, I.249, R.296, H.300, K.301, V.302 Ligands: T8T.14, MG.15 18 PLIP interactions: 7 interactions with chain C, 9 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: C:V.80, C:F.81 Hydrogen bonds: C:V.80, C:R.296, A:R.257, A:N.282, B:N.43, B:N.43 Salt bridges: C:H.300, C:K.301, C:K.301, A:D.254, A:R.276, A:K.278, A:K.278, A:K.447, A:K.447 pi-Cation interactions: A:R.257 T8T.14: 17 residues within 4Å: Chain A: K.447 Chain B: K.40, V.41, I.42, V.57, I.60, D.61, Q.66, R.69, F.89 Chain C: Y.79, V.80, V.302, R.375, K.379 Ligands: T8T.13, MG.15 13 PLIP interactions: 2 interactions with chain A, 5 interactions with chain C, 6 interactions with chain B Salt bridges: A:K.447, A:K.447, C:K.379, C:K.379, B:K.40, B:K.40, B:D.61 Hydrogen bonds: C:R.375, C:R.375, B:Q.66, B:R.69 pi-Cation interactions: C:R.375 Hydrophobic interactions: B:I.42 T8T.16: 18 residues within 4Å: Chain D: Q.73, L.74, R.88, D.131, H.134, H.139, H.157, E.158, D.235, K.236, Y.239, D.243, R.290, H.294, Y.298, Q.299, D.307 Ligands: MN.17 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:Y.298 Hydrogen bonds: D:Q.73, D:L.74, D:R.88, D:E.158, D:D.243, D:Q.299 Salt bridges: D:H.139, D:H.157, D:K.236, D:R.290, D:D.307 pi-Stacking: D:H.139, D:H.294 T8T.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, G.248, I.249, R.296, H.300, K.301 Ligands: T8T.19, MG.20 16 PLIP interactions: 6 interactions with chain D, 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: D:V.80, D:F.81 Hydrogen bonds: D:V.80, B:R.257, B:N.282, A:N.43, A:N.43 Salt bridges: D:H.300, D:K.301, D:K.301, B:D.254, B:R.276, B:K.278, B:K.278, B:K.447 pi-Cation interactions: B:R.257 T8T.19: 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, K.301, V.302, R.375 Ligands: T8T.18, MG.20 15 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B, 6 interactions with chain D Hydrophobic interactions: A:I.42 Hydrogen bonds: A:V.41, A:Q.66, A:R.69, D:R.375, D:R.375 Salt bridges: A:K.40, A:K.40, A:D.61, B:K.447, B:K.447, D:K.301, D:K.301, D:K.379 pi-Cation interactions: D:R.375

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

MN.2: 6 residues within 4Å: Chain A: R.88, H.91, H.130, D.131, D.235 Ligands: T8T.1 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:H.91, A:H.130, A:D.131, A:D.235, A:D.235 MN.7: 6 residues within 4Å: Chain B: R.88, H.91, H.130, D.131, D.235 Ligands: T8T.6 5 PLIP interactions: 5 interactions with chain B Metal complexes: B:H.91, B:H.130, B:D.131, B:D.235, B:D.235 MN.12: 6 residues within 4Å: Chain C: R.88, H.91, H.130, D.131, D.235 Ligands: T8T.11 5 PLIP interactions: 5 interactions with chain C Metal complexes: C:H.91, C:H.130, C:D.131, C:D.235, C:D.235 MN.17: 6 residues within 4Å: Chain D: R.88, H.91, H.130, D.131, D.235 Ligands: T8T.16 5 PLIP interactions: 5 interactions with chain D Metal complexes: D:H.91, D:H.130, D:D.131, D:D.235, D:D.235

4 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 4 residues within 4Å: Chain C: K.447 Chain D: K.40 Ligands: T8T.3, T8T.4 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain C: K.40 Chain D: K.447 Ligands: T8T.8, T8T.9 No protein-ligand interaction detected (PLIP) MG.15: 4 residues within 4Å: Chain A: K.447 Chain B: K.40 Ligands: T8T.13, T8T.14 No protein-ligand interaction detected (PLIP) MG.20: 3 residues within 4Å: Chain A: K.40 Ligands: T8T.18, T8T.19 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