SMTL ID : 5hml.2 (1 other biounit)

Crystal Structure of T5 D15 Protein Co-crystallized with Metal Ions

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.48 Å

Oligo State

monomer

Ligands

1 x B3P: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

B3P.1: 5 residues within 4Å: Chain A: E.163, H.164, N.166, A.195, K.196 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.163, A:H.164, A:N.166 Water bridges: A:K.196

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.136, D.185 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.136, A:D.185, H2O.1, H2O.2, H2O.8, H2O.9 MG.3: 1 residues within 4Å: Chain A: D.68 6 PLIP interactions: 1 interactions with chain A, 5 Ligand-Water interactions Metal complexes: A:D.68, H2O.1, H2O.2, H2O.3, H2O.5, H2O.11

9 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: G.194, A.195, K.196, R.197 Ligand excluded by PLIP CL.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.6: 2 residues within 4Å: Chain A: G.219, K.220 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: H.17, F.150 Ligand excluded by PLIP CL.8: 2 residues within 4Å: Chain A: K.16, N.19 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: P.23, A.25, S.26 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain A: F.85 Ligand excluded by PLIP CL.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.12: 6 residues within 4Å: Chain A: I.131, S.132, T.133, F.148, S.149, F.150 Ligand excluded by PLIP

2 x IOD: IODIDE ION(Non-functional Binders)

IOD.13: 1 residues within 4Å: Chain A: V.54 Ligand excluded by PLIP IOD.14: 3 residues within 4Å: Chain A: G.192, K.222, N.226 Ligand excluded by 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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Exodeoxyribonuclease

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