SMTL ID : 5bnh.1

Crystal structure of the HLTF HIRAN domain with a ssDNA fragment

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

1 x DG- DT- DG: DNA (5'-D(*(GD)P*GP*TP*G)-3')(Non-covalent)

DG-DT-DG.1: 13 residues within 4Å: Chain A: V.16, G.17, R.19, Y.20, Y.21, N.39, Y.41, D.42, A.45, H.58, L.59, K.60, K.61 Protein-ligand interaction information (PLIP) not available

1 x DT- DT- DG: DNA (5'-D(*(TD)P*TP*G)-3')(Non-covalent)

DT-DT-DG.2: 13 residues within 4Å: Chain B: V.16, G.17, R.19, Y.20, Y.21, N.39, Y.41, D.42, A.45, H.58, L.59, K.60, K.61 Protein-ligand interaction information (PLIP) not available

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 2 residues within 4Å: Chain A: L.18, Y.21 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.18, A:Y.21 NA.4: 3 residues within 4Å: Chain A: Y.21, Q.55 Ligands: PO4.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.55 Water bridges: A:Q.55

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 4 residues within 4Å: Chain A: G.53, N.54, Q.55 Ligands: NA.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.54, A:Q.55 PO4.6: 3 residues within 4Å: Chain A: R.12, P.83, H.95 3 PLIP interactions: 3 interactions with chain A Water bridges: A:H.95 Salt bridges: A:R.12, A:H.95

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.7: 4 residues within 4Å: Chain B: N.88, A.89, F.90, T.91 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:N.88, B:F.90 Hydrogen bonds: B:A.89 ACT.8: 5 residues within 4Å: Chain B: N.27, G.85, A.86, N.87, N.88 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.27, B:G.85, B:N.87, B:N.87, B:N.88, B:N.88 ACT.9: 2 residues within 4Å: Chain B: Q.111, H.115 4 PLIP interactions: 4 interactions with chain B Water bridges: B:N.44, B:N.44, B:Q.111 Salt bridges: B:H.115 ACT.10: 3 residues within 4Å: Chain B: G.13, H.14, K.60 3 PLIP interactions: 3 interactions with chain B Water bridges: B:H.14 Salt bridges: B:H.14, B:K.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Neculai, D. et al., Co-crystal structure of the HLTF HIRAN domain with a ssDNA fragment. To Be Published

Release Date

2016-05-25

Peptides

Helicase-like transcription factor: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
D

Helicase-like transcription factor