SMTL ID : 5k97.1

Flap endonuclease 1 (FEN1) D233N with cleaved product fragment and Sm3+

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

1 x DA- DC- DC- DG- DT- DC- DC: DNA (5'-D(*AP*CP*CP*GP*TP*CP*C)-3')(Non-covalent)

DA-DC-DC-DG-DT-DC-DC.1: 18 residues within 4Å: Chain A: R.46, Q.47, L.52, Q.53, N.54, T.60, M.64, K.313, Q.314, F.315, S.316, R.319 Chain B: G.13, A.14, C.15, G.16, G.17, T.18 Protein-ligand interaction information (PLIP) not available

1 x DT- DT: DNA (5'-D(P*TP*T)-3')(Non-covalent)

DT-DT.2: 12 residues within 4Å: Chain A: D.85, G.86, K.87, P.88, K.92, L.96, R.99, S.100, R.103, K.131, V.132 Chain C: T.1 Protein-ligand interaction information (PLIP) not available

8 x SM: SAMARIUM (III) ION(Non-covalent)

SM.3: 8 residues within 4Å: Chain A: G.1, E.159, D.178, D.180, N.232 Chain C: T.1 Ligands: SM.5, SM.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.159, A:D.180, A:D.180, H2O.8 SM.4: 6 residues within 4Å: Chain A: D.85, K.92, E.157, A.158, E.159 Ligands: SM.6 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.157, H2O.1, H2O.22 SM.5: 6 residues within 4Å: Chain A: G.1, E.159, D.178, D.180 Chain C: T.1 Ligands: SM.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:E.159, A:D.178, A:D.180 SM.6: 7 residues within 4Å: Chain A: D.33, K.92, E.157, E.159 Chain C: T.1 Ligands: SM.3, SM.4 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.159, A:E.159, H2O.1, H2O.21, H2O.22 SM.8: 2 residues within 4Å: Chain A: E.56, E.312 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.56, A:E.56, A:E.312, H2O.4 SM.9: 5 residues within 4Å: Chain A: N.54, E.56, E.58, E.312, K.313 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.56, A:E.58, A:E.58, A:E.312 SM.10: 2 residues within 4Å: Chain A: G.48, D.50 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.48, A:D.50, H2O.12 SM.11: 2 residues within 4Å: Chain A: K.98, E.101 No protein-ligand interaction detected (PLIP)

1 x K: POTASSIUM ION(Non-covalent)

K.7: 5 residues within 4Å: Chain A: S.236, I.237, R.238, I.240 Chain B: T.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:S.236, A:I.237, H2O.6, H2O.19

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.12: 10 residues within 4Å: Chain A: G.1, I.2, L.5, E.177, D.178, M.179, D.180 Chain C: T.1, G.2, A.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:I.2, A:I.2, A:M.179 Water bridges: A:L.5, A:E.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsutakawa, S.E. et al., Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability. Nat Commun (2017)

Release Date

2017-06-28

Peptides

Flap endonuclease 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Flap endonuclease 1