- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.15 Å
- Oligo State
- homo-trimer
- Ligands
- 3 x ACY: ACETIC ACID(Non-functional Binders)
- 6 x MG: MAGNESIUM ION(Non-covalent)
MG.2: 8 residues within 4Å:- Chain A: D.168
- Chain B: D.168
- Chain C: D.168
- Ligands: NA.5, MG.7, NA.10, MG.12, NA.15
6 PLIP interactions:1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions- Metal complexes: C:D.168, B:D.168, A:D.168, H2O.1, H2O.7, H2O.13
MG.3: 5 residues within 4Å:- Chain A: E.185
- Chain B: E.185
- Chain C: E.185
- Ligands: MG.8, MG.13
3 PLIP interactions:1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B- Metal complexes: A:E.185, C:E.185, B:E.185
MG.7: 8 residues within 4Å:- Chain A: D.168
- Chain B: D.168
- Chain C: D.168
- Ligands: MG.2, NA.5, NA.10, MG.12, NA.15
6 PLIP interactions:1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions- Metal complexes: C:D.168, B:D.168, A:D.168, H2O.1, H2O.7, H2O.13
MG.8: 5 residues within 4Å:- Chain A: E.185
- Chain B: E.185
- Chain C: E.185
- Ligands: MG.3, MG.13
3 PLIP interactions:1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B- Metal complexes: A:E.185, C:E.185, B:E.185
MG.12: 8 residues within 4Å:- Chain A: D.168
- Chain B: D.168
- Chain C: D.168
- Ligands: MG.2, NA.5, MG.7, NA.10, NA.15
6 PLIP interactions:1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions- Metal complexes: C:D.168, B:D.168, A:D.168, H2O.1, H2O.7, H2O.13
MG.13: 5 residues within 4Å:- Chain A: E.185
- Chain B: E.185
- Chain C: E.185
- Ligands: MG.3, MG.8
3 PLIP interactions:1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B- Metal complexes: A:E.185, C:E.185, B:E.185
- 3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
MPD.4: 6 residues within 4Å:- Chain A: H.96, R.97, V.158, P.159, T.160
- Chain C: E.130
3 PLIP interactions:2 interactions with chain A, 1 interactions with chain C- Hydrogen bonds: A:T.160, A:T.160
- Hydrophobic interactions: C:E.130
MPD.9: 6 residues within 4Å:- Chain A: E.130
- Chain B: H.96, R.97, V.158, P.159, T.160
3 PLIP interactions:1 interactions with chain A, 2 interactions with chain B- Hydrophobic interactions: A:E.130
- Hydrogen bonds: B:T.160, B:T.160
MPD.14: 6 residues within 4Å:- Chain B: E.130
- Chain C: H.96, R.97, V.158, P.159, T.160
3 PLIP interactions:1 interactions with chain B, 2 interactions with chain C- Hydrophobic interactions: B:E.130
- Hydrogen bonds: C:T.160, C:T.160
- 3 x NA: SODIUM ION(Non-functional Binders)
NA.5: 11 residues within 4Å:- Chain A: D.166, D.168
- Chain B: D.166, D.168
- Chain C: D.166, D.168
- Ligands: MG.2, MG.7, NA.10, MG.12, NA.15
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:D.166
NA.10: 11 residues within 4Å:- Chain A: D.166, D.168
- Chain B: D.166, D.168
- Chain C: D.166, D.168
- Ligands: MG.2, NA.5, MG.7, MG.12, NA.15
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:D.166
NA.15: 11 residues within 4Å:- Chain A: D.166, D.168
- Chain B: D.166, D.168
- Chain C: D.166, D.168
- Ligands: MG.2, NA.5, MG.7, NA.10, MG.12
1 PLIP interactions:1 interactions with chain C- Hydrogen bonds: C:D.166
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Schuldt, L. et al., The three-dimensional Structure of a mycobacterial DapD provides insights into DapD diversity and reveals unexpected particulars about the enzymatic mechanism. J.Mol.Biol. (2009)
- Release Date
- 2009-06-23
- Peptides
- Tetrahydrodipicolinate N-succinyltransferase: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
DB
DC
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.15 Å
- Oligo State
- homo-trimer
- Ligands
- 3 x ACY: ACETIC ACID(Non-functional Binders)
- 6 x MG: MAGNESIUM ION(Non-covalent)
- 3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)
- 3 x NA: SODIUM ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Schuldt, L. et al., The three-dimensional Structure of a mycobacterial DapD provides insights into DapD diversity and reveals unexpected particulars about the enzymatic mechanism. J.Mol.Biol. (2009)
- Release Date
- 2009-06-23
- Peptides
- Tetrahydrodipicolinate N-succinyltransferase: ABC
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
DB
DC
D