SMTL ID : 5hp4.1

Crystal structure bacteriohage T5 D15 flap endonuclease (D155K) pseudo-enzyme-product complex with DNA and metal ions

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

monomer

Ligands

4 x CA: CALCIUM ION(Non-functional Binders)(Non-covalent)

CA.1: 1 residues within 4Å: Chain A: C.15 No protein-ligand interaction detected (PLIP) CA.4: 3 residues within 4Å: Chain B: E.109, D.111, D.134 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.109, B:D.111, H2O.2, H2O.3, H2O.7 CA.6: 1 residues within 4Å: Chain C: C.15 No protein-ligand interaction detected (PLIP) CA.9: 1 residues within 4Å: Chain D: C.15 No protein-ligand interaction detected (PLIP)

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

NA.2: 4 residues within 4Å: Chain A: T.7, A.8 Chain D: C.4, T.5 No protein-ligand interaction detected (PLIP) NA.7: 2 residues within 4Å: Chain C: T.7, A.8 No protein-ligand interaction detected (PLIP) NA.10: 4 residues within 4Å: Chain A: C.4, T.5 Chain D: T.7, A.8 No protein-ligand interaction detected (PLIP)

3 x K: POTASSIUM ION(Non-covalent)(Non-functional Binders)

K.3: 4 residues within 4Å: Chain A: T.5 Chain B: M.180, V.190, I.193 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:V.190, B:I.193, H2O.1 K.8: 1 residues within 4Å: Chain C: T.5 No protein-ligand interaction detected (PLIP) K.11: 1 residues within 4Å: Chain D: T.5 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain B: T.9, G.48, D.49, L.89, K.90, F.93, T.104 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

AlMalki, F.A. et al., Direct observation of DNA threading in flap endonuclease complexes. Nat.Struct.Mol.Biol. (2016)

Release Date

2016-06-01

Peptides

Exodeoxyribonuclease: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

B
A

Exodeoxyribonuclease