- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.70 Å
- Oligo State
- homo-hexamer
- Ligands
- 9 x KGA: [1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethoxy]-1-oxidanylidene-propan-2-ylidene]-bis(oxidanidyl)azanium(Non-covalent)
- 3 x NI: NICKEL (II) ION(Non-covalent)
NI.2: 4 residues within 4Å:- Chain A: H.220
- Chain B: H.220
- Chain C: H.220
- Ligands: IMD.3
5 PLIP interactions:1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C, 2 Ligand-Water interactions- Metal complexes: B:H.220, A:H.220, C:H.220, H2O.9, H2O.22
NI.9: 3 residues within 4Å:- Chain D: H.220
- Chain E: H.220
- Chain F: H.220
6 PLIP interactions:1 interactions with chain E, 1 interactions with chain F, 1 interactions with chain D, 3 Ligand-Water interactions- Metal complexes: E:H.220, F:H.220, D:H.220, H2O.42, H2O.58, H2O.72
NI.15: 4 residues within 4Å:- Chain F: E.241, H.261
- Ligands: KG7.17, IMD.18
3 PLIP interactions:2 interactions with chain F, 1 Ligand-Water interactions- Metal complexes: F:E.241, F:H.261, H2O.69
- 3 x IMD: IMIDAZOLE(Non-covalent)
IMD.3: 4 residues within 4Å:- Chain B: H.220
- Chain C: F.154, H.220
- Ligands: NI.2
No protein-ligand interaction detected (PLIP)IMD.11: 7 residues within 4Å:- Chain D: V.9, T.10, I.11, V.14, V.16, L.192, H.196
1 PLIP interactions:1 interactions with chain D- Hydrogen bonds: D:H.196
IMD.18: 5 residues within 4Å:- Chain F: E.241, V.259, H.261
- Ligands: NI.15, KG7.17
2 PLIP interactions:2 interactions with chain F- Water bridges: F:E.241, F:N.257
- 1 x K: POTASSIUM ION(Non-covalent)
- 1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
- 1 x KG7: (2E)-2-(hydroxyimino)propanoic acid(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Stunkard, L.M. et al., Sulfonate/Nitro Bearing Methylmalonyl-Thioester Isosteres Applied to Methylmalonyl-CoA Decarboxylase Structure-Function Studies. J. Am. Chem. Soc. (2019)
- Release Date
- 2019-04-10
- Peptides
- Methylmalonyl-CoA decarboxylase: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
F
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.70 Å
- Oligo State
- homo-hexamer
- Ligands
- 9 x KGA: [1-[2-[3-[[(2~{R})-4-[[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-3-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-3,3-dimethyl-2-oxidanyl-butanoyl]amino]propanoylamino]ethoxy]-1-oxidanylidene-propan-2-ylidene]-bis(oxidanidyl)azanium(Non-covalent)
- 3 x NI: NICKEL (II) ION(Non-covalent)
- 3 x IMD: IMIDAZOLE(Non-covalent)
- 1 x K: POTASSIUM ION(Non-covalent)
- 1 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)
- 1 x KG7: (2E)-2-(hydroxyimino)propanoic acid(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Stunkard, L.M. et al., Sulfonate/Nitro Bearing Methylmalonyl-Thioester Isosteres Applied to Methylmalonyl-CoA Decarboxylase Structure-Function Studies. J. Am. Chem. Soc. (2019)
- Release Date
- 2019-04-10
- Peptides
- Methylmalonyl-CoA decarboxylase: ABCDEF
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
AB
BC
CD
DE
EF
F