- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.67 Å
- Oligo State
- homo-dimer
- Ligands
- 4 x DAL: D-ALANINE(Non-covalent)
- 4 x MG: MAGNESIUM ION(Non-covalent)
MG.3: 5 residues within 4Å:- Chain A: K.230, E.284
- Ligands: MG.4, ADP.6, CO3.7
3 PLIP interactions:1 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:E.284, H2O.1, H2O.4
MG.4: 6 residues within 4Å:- Chain A: E.284, N.286
- Ligands: MG.3, K.5, ADP.6, CO3.7
3 PLIP interactions:2 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:E.284, A:E.284, H2O.3
MG.10: 6 residues within 4Å:- Chain B: K.230, D.272, E.284
- Ligands: MG.11, ADP.13, CO3.14
3 PLIP interactions:1 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:E.284, H2O.9, H2O.12
MG.11: 6 residues within 4Å:- Chain B: E.284, N.286
- Ligands: MG.10, K.12, ADP.13, CO3.14
3 PLIP interactions:2 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:E.284, B:E.284, H2O.12
- 2 x K: POTASSIUM ION(Non-covalent)
K.5: 6 residues within 4Å:- Chain A: C.115, M.116, E.284, L.285, N.286
- Ligands: MG.4
5 PLIP interactions:3 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:C.115, A:E.284, A:L.285, H2O.2, H2O.4
K.12: 6 residues within 4Å:- Chain B: C.115, M.116, E.284, L.285, N.286
- Ligands: MG.11
5 PLIP interactions:3 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:C.115, B:E.284, B:L.285, H2O.10, H2O.12
- 2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
ADP.6: 24 residues within 4Å:- Chain A: K.118, V.133, F.153, K.155, T.159, G.160, S.161, S.162, I.165, E.191, K.192, A.193, L.194, E.199, Y.220, F.224, Y.225, K.230, F.274, N.283, E.284
- Ligands: MG.3, MG.4, CO3.7
23 PLIP interactions:23 interactions with chain A- Hydrogen bonds: A:K.155, A:G.160, A:S.161, A:S.162, A:E.191, A:E.191, A:L.194, A:E.199, A:Y.225, A:N.283
- Water bridges: A:K.118, A:K.155, A:E.199, A:K.230, A:K.230, A:D.272
- Salt bridges: A:K.118, A:K.118, A:K.155, A:K.230, A:K.230
- pi-Stacking: A:F.153, A:F.153
ADP.13: 24 residues within 4Å:- Chain B: K.118, V.133, F.153, K.155, T.159, G.160, S.161, S.162, I.165, E.191, K.192, A.193, L.194, E.199, Y.220, F.224, Y.225, K.230, F.274, N.283, E.284
- Ligands: MG.10, MG.11, CO3.14
20 PLIP interactions:20 interactions with chain B- Hydrogen bonds: B:K.155, B:S.161, B:S.162, B:E.191, B:L.194, B:E.199, B:Y.225, B:N.283
- Water bridges: B:E.199, B:E.199, B:Y.220, B:K.230, B:K.230
- Salt bridges: B:K.118, B:K.118, B:K.155, B:K.230, B:K.230
- pi-Stacking: B:F.153, B:F.153
- 2 x CO3: CARBONATE ION(Non-functional Binders)
CO3.7: 12 residues within 4Å:- Chain A: G.160, S.161, K.230, R.270, D.272, E.284, N.286
- Ligands: DAL.1, DAL.2, MG.3, MG.4, ADP.6
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:K.230, A:R.270, A:D.272
CO3.14: 12 residues within 4Å:- Chain B: G.160, S.161, K.230, R.270, D.272, E.284, N.286
- Ligands: DAL.8, DAL.9, MG.10, MG.11, ADP.13
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:S.161, B:K.230, B:E.284
- Water bridges: B:R.270
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Pederick, J.L. et al., d-Alanine-d-alanine ligase as a model for the activation of ATP-grasp enzymes by monovalent cations. J.Biol.Chem. (2020)
- Release Date
- 2020-05-06
- Peptides
- D-alanine--D-alanine ligase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
CB
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.67 Å
- Oligo State
- homo-dimer
- Ligands
- 4 x DAL: D-ALANINE(Non-covalent)
- 4 x MG: MAGNESIUM ION(Non-covalent)
- 2 x K: POTASSIUM ION(Non-covalent)
- 2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
- 2 x CO3: CARBONATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Pederick, J.L. et al., d-Alanine-d-alanine ligase as a model for the activation of ATP-grasp enzymes by monovalent cations. J.Biol.Chem. (2020)
- Release Date
- 2020-05-06
- Peptides
- D-alanine--D-alanine ligase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
CB
D