SMTL ID : 5b42.1

Crystal structure of the C-terminal endonuclease domain of Aquifex aeolicus MutL.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

12 x CD: CADMIUM ION(Non-covalent)

CD.1: 5 residues within 4Å: Chain A: H.30, E.34, C.48 Ligands: CD.2, CD.5 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.30, A:E.34, A:C.48, H2O.3, H2O.3, H2O.4 CD.2: 5 residues within 4Å: Chain A: L.31, E.34, C.79, H.81 Ligands: CD.1 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.34, A:C.79, A:H.81, H2O.2, H2O.3 CD.3: 1 residues within 4Å: Chain A: E.61 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.61, A:E.61, H2O.3, H2O.4 CD.4: 1 residues within 4Å: Chain A: D.43 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.43, A:D.43, H2O.3, H2O.4 CD.5: 2 residues within 4Å: Chain A: C.48 Ligands: CD.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:C.48, H2O.1, H2O.3, H2O.4, H2O.4 CD.8: 2 residues within 4Å: Chain A: E.93, E.96 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.93, A:E.96, A:E.96, H2O.2, H2O.3 CD.9: 5 residues within 4Å: Chain B: H.30, E.34, C.48 Ligands: CD.10, CD.13 6 PLIP interactions: 3 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:H.30, B:E.34, B:C.48, H2O.7, H2O.7, H2O.7 CD.10: 5 residues within 4Å: Chain B: L.31, E.34, C.79, H.81 Ligands: CD.9 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.34, B:C.79, B:H.81, H2O.6, H2O.7 CD.11: 1 residues within 4Å: Chain B: E.61 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.61, B:E.61, H2O.7, H2O.7 CD.12: 1 residues within 4Å: Chain B: D.43 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.43, B:D.43, H2O.7, H2O.7 CD.13: 2 residues within 4Å: Chain B: C.48 Ligands: CD.9 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:C.48, H2O.4, H2O.7, H2O.7, H2O.8 CD.16: 2 residues within 4Å: Chain B: E.93, E.96 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.93, B:E.96, B:E.96, H2O.6, H2O.7

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 7 residues within 4Å: Chain A: K.2, Y.5, V.18, D.20, Y.25, W.70 Ligands: PEG.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.2, A:Y.25 Water bridges: A:R.71 PEG.7: 7 residues within 4Å: Chain A: Y.25, W.70, R.71, P.76, H.77, Y.86 Ligands: PEG.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.25, A:R.71, A:Y.86 PEG.14: 7 residues within 4Å: Chain B: K.2, Y.5, V.18, D.20, Y.25, W.70 Ligands: PEG.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.20 Water bridges: B:R.71 PEG.15: 7 residues within 4Å: Chain B: Y.25, W.70, R.71, P.76, H.77, Y.86 Ligands: PEG.14 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.71, B:Y.86

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fukui, K. et al., Structural Features and Functional Dependency on beta-Clamp Define Distinct Subfamilies of Bacterial Mismatch Repair Endonuclease MutL. J.Biol.Chem. (2016)

Release Date

2016-07-13

Peptides

DNA mismatch repair protein MutL: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

DNA mismatch repair protein MutL

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