SMTL ID : 4qg4.1

Crystal structure of the tetrameric GTP/dATP/ATP-bound SAMHD1 (H210A) mutant catalytic core

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

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

GTP.1: 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: DTP.11, MG.15 17 PLIP interactions: 8 interactions with chain D, 2 interactions with chain C, 7 interactions with chain A Hydrogen bonds: D:V.41, D:Q.66, D:R.69, A:R.375 Water bridges: D:D.61, A:K.379 Salt bridges: D:K.40, D:K.40, D:K.40, D:D.61, C:K.447, C:K.447, A:K.301, A:R.375, A:K.379, A:K.379 pi-Cation interactions: A:R.375 GTP.3: 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: MG.4, DTP.8 19 PLIP interactions: 2 interactions with chain B, 6 interactions with chain D, 11 interactions with chain A Salt bridges: B:K.447, B:K.447, D:R.375, D:K.379, D:K.379, A:K.40, A:K.40, A:K.40, A:D.61 Hydrogen bonds: D:R.375, A:V.41, A:Q.66, A:R.69 Water bridges: D:K.379, A:K.40, A:K.40, A:K.40, A:K.40 pi-Cation interactions: D:R.375 GTP.6: 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: MG.12, DTP.14 19 PLIP interactions: 7 interactions with chain B, 10 interactions with chain C, 2 interactions with chain D Hydrogen bonds: B:R.375, C:V.41, C:Q.66, C:R.69 Water bridges: B:K.379, B:K.379, C:K.40, C:K.40, C:K.40 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 GTP.7: 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: DTP.2, MG.9 17 PLIP interactions: 10 interactions with chain B, 5 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:V.41, B:Q.66, B:R.69 Water bridges: B:K.40, B:K.40, B:K.40, C:K.379 Salt bridges: B:K.40, B:K.40, B:K.40, B:D.61, C:R.375, C:K.379, C:K.379, A:K.447, A:K.447 pi-Cation interactions: C:R.375

4 x DTP: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE(Non-covalent)

DTP.2: 19 residues within 4Å: Chain A: 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: GTP.7, MG.9 24 PLIP interactions: 9 interactions with chain C, 13 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: C:V.80, C:F.81 Water bridges: C:K.301, C:K.301, A:K.278, A:K.278 Salt bridges: C:H.300, C:H.300, C:K.301, C:K.301, C:K.301, A:R.257, A:R.276, A:K.278, A:K.278, A:K.278, A:K.447 Hydrogen bonds: A:R.257, A:N.282, A:N.282, B:N.43, B:N.43 pi-Cation interactions: A:R.257, A:R.257 DTP.8: 18 residues within 4Å: Chain A: V.41, I.42, N.43, H.49 Chain B: R.257, F.261, R.276, K.278, N.282, K.447 Chain D: V.80, F.81, R.296, H.300, K.301, V.302 Ligands: GTP.3, MG.4 27 PLIP interactions: 17 interactions with chain B, 3 interactions with chain A, 7 interactions with chain D Hydrogen bonds: B:R.257, B:N.282, B:N.282, A:N.43, A:N.43 Water bridges: B:D.254, B:R.257, B:R.257, B:R.257, B:E.279, B:K.447, A:K.40 Salt bridges: 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 DTP.11: 19 residues within 4Å: Chain A: V.80, F.81, I.249, R.296, H.300, K.301, V.302 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: GTP.1, MG.15 21 PLIP interactions: 13 interactions with chain C, 6 interactions with chain A, 2 interactions with chain D Hydrogen bonds: C:R.257, C:N.282, C:N.282, D:N.43, D:N.43 Water bridges: C:R.257, C:R.257 Salt bridges: 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 pi-Cation interactions: C:R.257, C:R.257 Hydrophobic interactions: A:V.80, A:F.81 DTP.14: 19 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: R.257, F.261, R.276, K.278, N.282, K.447 Ligands: GTP.6, MG.12 26 PLIP interactions: 17 interactions with chain D, 7 interactions with chain B, 2 interactions with chain C Hydrogen bonds: D:R.257, D:N.282, D:N.282, C:N.43, C:N.43 Water bridges: D:R.257, D:R.257, D:K.278, D:K.278, D:K.278, D:K.278 Salt bridges: 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

4 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 4 residues within 4Å: Chain A: K.40 Chain B: K.447 Ligands: GTP.3, DTP.8 No protein-ligand interaction detected (PLIP) MG.9: 3 residues within 4Å: Chain B: K.40 Ligands: DTP.2, GTP.7 No protein-ligand interaction detected (PLIP) MG.12: 3 residues within 4Å: Chain C: K.40 Ligands: GTP.6, DTP.14 No protein-ligand interaction detected (PLIP) MG.15: 3 residues within 4Å: Chain D: K.40 Ligands: GTP.1, DTP.11 No protein-ligand interaction detected (PLIP)

4 x ZN: ZINC ION(Non-covalent)

ZN.5: 5 residues within 4Å: Chain A: R.88, H.91, H.130, D.131, D.235 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.91, A:H.130, A:D.131, A:D.235 ZN.10: 5 residues within 4Å: Chain B: R.88, H.91, H.130, D.131, D.235 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.91, B:H.130, B:D.235 ZN.13: 5 residues within 4Å: Chain C: R.88, H.91, H.130, D.131, D.235 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.91, C:H.130, C:D.131, C:D.235, H2O.15 ZN.16: 5 residues within 4Å: Chain D: R.88, H.91, H.130, D.131, D.235 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Koharudin, L.M. et al., Structural Basis of Allosteric Activation of Sterile alpha Motif and Histidine-Aspartate Domain-containing Protein 1 (SAMHD1) by Nucleoside Triphosphates. J.Biol.Chem. (2014)

Release Date

2014-10-15

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