SMTL ID : 3fsy.3 (2 other biounits)

Structure of tetrahydrodipicolinate N-succinyltransferase (Rv1201c;DapD) in complex with succinyl-CoA from Mycobacterium tuberculosis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-trimer

Ligands

3 x SCA: SUCCINYL-COENZYME A(Non-covalent)

SCA.1: 22 residues within 4Å: Chain A: E.201, G.217, G.218, L.241, G.243, A.244, V.257, E.259, A.260, R.292, R.293, N.294, S.295 Chain B: R.203, S.205, S.221, I.222, M.223, T.265, G.267, K.279, R.281 18 PLIP interactions: 10 interactions with chain A, 8 interactions with chain B Hydrophobic interactions: A:L.241, A:V.257, A:E.259 Hydrogen bonds: A:A.244, A:E.259, A:A.260, A:R.292, A:R.293, A:S.295, B:T.265, B:G.267, B:K.279, B:R.281 pi-Cation interactions: A:R.292 Water bridges: B:S.205, B:G.267 Salt bridges: B:R.203, B:K.279 SCA.6: 22 residues within 4Å: Chain B: E.201, G.217, G.218, L.241, G.243, A.244, V.257, E.259, A.260, R.292, R.293, N.294, S.295 Chain C: R.203, S.205, S.221, I.222, M.223, T.265, G.267, K.279, R.281 18 PLIP interactions: 10 interactions with chain B, 8 interactions with chain C Hydrophobic interactions: B:L.241, B:V.257, B:E.259 Hydrogen bonds: B:A.244, B:E.259, B:A.260, B:R.292, B:R.293, B:S.295, C:G.267, C:K.279, C:R.281 pi-Cation interactions: B:R.292 Water bridges: C:S.205, C:T.265, C:G.267 Salt bridges: C:R.203, C:K.279 SCA.11: 22 residues within 4Å: Chain A: R.203, S.205, S.221, I.222, M.223, T.265, G.267, K.279, R.281 Chain C: E.201, G.217, G.218, L.241, G.243, A.244, V.257, E.259, A.260, R.292, R.293, N.294, S.295 17 PLIP interactions: 9 interactions with chain C, 8 interactions with chain A Hydrophobic interactions: C:L.241, C:V.257, C:E.259 Hydrogen bonds: C:A.244, C:A.260, C:R.292, C:R.293, C:S.295, A:G.267, A:K.279, A:R.281 pi-Cation interactions: C:R.292 Water bridges: A:S.205, A:T.265, A:G.267 Salt bridges: A:R.203, A:K.279

9 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 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:D.168, A:D.168, H2O.1, H2O.1, H2O.2 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 C, 1 interactions with chain B, 1 interactions with chain A Metal complexes: C:E.185, B:E.185, A:E.185 MG.4: 5 residues within 4Å: Chain A: S.297 Chain B: S.297 Chain C: S.297 Ligands: MG.9, MG.14 No protein-ligand interaction detected (PLIP) 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 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: B:D.168, C:D.168, H2O.1, H2O.1, H2O.2 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 C, 1 interactions with chain B, 1 interactions with chain A Metal complexes: C:E.185, B:E.185, A:E.185 MG.9: 5 residues within 4Å: Chain A: S.297 Chain B: S.297 Chain C: S.297 Ligands: MG.4, MG.14 No protein-ligand interaction detected (PLIP) 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 5 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: C:D.168, A:D.168, H2O.1, H2O.1, H2O.2 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 C, 1 interactions with chain B, 1 interactions with chain A Metal complexes: C:E.185, B:E.185, A:E.185 MG.14: 5 residues within 4Å: Chain A: S.297 Chain B: S.297 Chain C: S.297 Ligands: MG.4, MG.9 No protein-ligand interaction detected (PLIP)

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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.166, A:D.168 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 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.166, A:D.168 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 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:D.166, A:D.168

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
E

B
E

C
E

Tetrahydrodipicolinate N-succinyltransferase

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