- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.42 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x ZN: ZINC ION(Non-covalent)
- 1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)
AMP.2: 16 residues within 4Å:- Chain A: G.214, A.215, E.216, P.217, N.236, S.237, F.238, G.239, M.240, T.241, D.305, I.326, R.329, I.335, N.340
- Ligands: K.4
12 PLIP interactions:12 interactions with chain A- Hydrogen bonds: A:A.215, A:S.237, A:G.239, A:T.241, A:D.305, A:R.329
- Water bridges: A:T.143, A:N.236, A:T.241, A:T.241, A:T.241, A:T.303
- 1 x COA: COENZYME A(Non-covalent)
COA.3: 12 residues within 4Å:- Chain A: S.136, A.164, G.165, N.166, S.167, I.185, Y.188, R.191, K.337, V.407, T.408
- Ligands: SO4.6
14 PLIP interactions:14 interactions with chain A- Hydrogen bonds: A:G.165, A:N.166, A:S.167, A:S.167, A:K.337, A:Q.370, A:T.408, A:T.408
- Water bridges: A:I.185
- Salt bridges: A:R.191, A:K.337, A:K.337, A:K.402
- pi-Stacking: A:Y.188
- 3 x K: POTASSIUM ION(Non-covalent)
K.4: 5 residues within 4Å:- Chain A: A.215, I.335, G.338, N.340
- Ligands: AMP.2
2 PLIP interactions:2 interactions with chain A- Metal complexes: A:A.215, A:G.338
K.5: 8 residues within 4Å:- Chain A: M.84, K.85, R.86, G.88
- Chain B: K.129, G.156, C.157, L.158
5 PLIP interactions:2 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: B:K.129, B:G.156, A:K.85, A:G.88, H2O.1
K.13: 7 residues within 4Å:- Chain A: K.129, G.156, C.157, L.158
- Chain B: M.84, K.85, G.88
5 PLIP interactions:2 interactions with chain B, 2 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: B:K.85, B:G.88, A:K.129, A:G.156, H2O.10
- 3 x SO4: SULFATE ION(Non-functional Binders)
SO4.6: 5 residues within 4Å:- Chain A: N.166, S.167, Y.188, R.191
- Ligands: COA.3
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:N.166, A:S.167
- Salt bridges: A:R.191
SO4.7: 2 residues within 4Å:- Chain A: R.394, R.395
3 PLIP interactions:3 interactions with chain A- Salt bridges: A:R.394, A:R.395, A:K.410
SO4.15: 5 residues within 4Å:- Chain B: G.165, N.166, S.167, Y.188, R.191
6 PLIP interactions:6 interactions with chain B- Hydrogen bonds: B:N.166, B:S.167, B:S.167, B:S.167
- Water bridges: B:K.168
- Salt bridges: B:R.191
- 5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.8: 3 residues within 4Å:- Chain A: Y.6, W.7, Y.123
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:W.7, A:Y.123
EDO.9: 2 residues within 4Å:- Chain A: I.33, E.294
No protein-ligand interaction detected (PLIP)EDO.10: 5 residues within 4Å:- Chain A: T.67, K.68, S.69, R.304, D.331
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:K.68, A:S.69, A:R.304, A:D.331
EDO.16: 4 residues within 4Å:- Chain B: R.61, K.62, P.64, R.300
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:R.300
EDO.17: 3 residues within 4Å:- Chain B: W.7, E.8, N.116
2 PLIP interactions:2 interactions with chain B- Hydrogen bonds: B:W.7
- Water bridges: B:E.8
- 1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
ADP.12: 16 residues within 4Å:- Chain B: T.143, G.214, A.215, E.216, P.217, N.236, S.237, F.238, G.239, M.240, T.241, D.305, I.326, R.329, K.425
- Ligands: PEG.14
13 PLIP interactions:13 interactions with chain B- Hydrogen bonds: B:A.215, B:S.237, B:G.239, B:T.241, B:T.241, B:D.305, B:R.329, B:K.425
- Water bridges: B:N.236, B:G.239, B:I.326
- Salt bridges: B:K.425, B:K.425
- 1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Joint Center for Structural Genomics (JCSG), Crystal structure of a Hypothetical Acyl-CoA ligase (BT_0428) from Bacteroides thetaiotaomicron VPI-5482 at 2.42 A resolution. To be published
- Release Date
- 2014-08-27
- Peptides
- Phenylacetate-coenzyme A ligase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
CB
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.42 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x ZN: ZINC ION(Non-covalent)
- 1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)
- 1 x COA: COENZYME A(Non-covalent)
- 3 x K: POTASSIUM ION(Non-covalent)
- 3 x SO4: SULFATE ION(Non-functional Binders)
- 5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 1 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)
- 1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Joint Center for Structural Genomics (JCSG), Crystal structure of a Hypothetical Acyl-CoA ligase (BT_0428) from Bacteroides thetaiotaomicron VPI-5482 at 2.42 A resolution. To be published
- Release Date
- 2014-08-27
- Peptides
- Phenylacetate-coenzyme A ligase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
CB
D