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

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-trimer

Ligands

3 x ACY: ACETIC ACID(Non-functional Binders)

ACY.1: 7 residues within 4Å: Chain A: R.203, S.205, S.221, I.222, G.224 Chain B: G.218, A.244 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:R.203 Hydrogen bonds: A:S.221 Water bridges: A:T.225, B:G.218 Salt bridges: A:R.203 ACY.6: 7 residues within 4Å: Chain B: R.203, S.205, S.221, I.222, G.224 Chain C: G.218, A.244 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:R.203 Hydrogen bonds: B:S.221 Water bridges: B:T.225, C:G.218 Salt bridges: B:R.203 ACY.11: 7 residues within 4Å: Chain A: G.218, A.244 Chain C: R.203, S.205, S.221, I.222, G.224 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:R.203 Hydrogen bonds: C:S.221 Water bridges: C:T.225, A:G.218 Salt bridges: C:R.203

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 7 residues within 4Å: Chain A: H.96, R.97, V.157, V.158, P.159, T.160 Chain C: E.130 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: A:V.157, A:T.160, C:E.130 Hydrogen bonds: A:T.160, A:T.160 MPD.7: 7 residues within 4Å: Chain A: E.130 Chain B: H.96, R.97, V.157, V.158, P.159, T.160 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:V.157, B:T.160, A:E.130 Hydrogen bonds: B:T.160, B:T.160 MPD.12: 7 residues within 4Å: Chain B: E.130 Chain C: H.96, R.97, V.157, V.158, P.159, T.160 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:E.130, C:V.157, C:T.160 Hydrogen bonds: C:T.160, C:T.160

6 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 8 residues within 4Å: Chain A: D.168 Chain B: D.168 Chain C: D.168 Ligands: NA.5, MG.8, NA.10, MG.13, 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.8, H2O.16 MG.4: 5 residues within 4Å: Chain A: E.185 Chain B: E.185 Chain C: E.185 Ligands: MG.9, MG.14 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:E.185, C:E.185, A:E.185, H2O.7, H2O.23 MG.8: 8 residues within 4Å: Chain A: D.168 Chain B: D.168 Chain C: D.168 Ligands: MG.3, NA.5, NA.10, MG.13, 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.8, H2O.16 MG.9: 5 residues within 4Å: Chain A: E.185 Chain B: E.185 Chain C: E.185 Ligands: MG.4, MG.14 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:E.185, C:E.185, A:E.185, H2O.7, H2O.23 MG.13: 8 residues within 4Å: Chain A: D.168 Chain B: D.168 Chain C: D.168 Ligands: MG.3, NA.5, MG.8, 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.8, H2O.16 MG.14: 5 residues within 4Å: Chain A: E.185 Chain B: E.185 Chain C: E.185 Ligands: MG.4, MG.9 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:E.185, C:E.185, A:E.185, H2O.7, H2O.23

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.3, MG.8, NA.10, MG.13, NA.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.168, 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.3, NA.5, MG.8, MG.13, NA.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A: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.3, NA.5, MG.8, NA.10, MG.13 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:D.168, B: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
D

B
D

C
D

Tetrahydrodipicolinate N-succinyltransferase

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