SMTL ID : 3fsx.1 (2 other biounits)

Structure of tetrahydrodipicolinate N-succinyltransferase (Rv1201c; DapD) from Mycobacterium tuberculosis

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-trimer

Ligands

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

ACY.1: 6 residues within 4Å: Chain A: R.203, S.205, S.221, I.222 Chain C: G.218, A.244 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain A Water bridges: C:G.218, C:G.218 Hydrogen bonds: A:S.221 Salt bridges: A:R.203 ACY.6: 8 residues within 4Å: Chain A: G.218, A.244 Chain B: R.203, S.205, S.221, I.222, M.223, G.224 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Water bridges: A:G.218, A:G.218 Salt bridges: B:R.203 ACY.10: 8 residues within 4Å: Chain B: G.218, A.244 Chain C: R.203, S.205, S.221, I.222, M.223, G.224 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain B Water bridges: C:S.205, C:T.225, B:G.218 Salt bridges: C:R.203

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

MPD.2: 6 residues within 4Å: Chain A: H.96, R.97, V.158, P.159, T.160 Chain B: E.130 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.160, A:T.160 Hydrophobic interactions: B:E.130 MPD.9: 6 residues within 4Å: Chain B: H.96, R.97, V.158, P.159, T.160 Chain C: E.130 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:E.130 Hydrogen bonds: B:T.160, B:T.160 Water bridges: B:R.97

4 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 6 residues within 4Å: Chain A: R.169, E.185 Chain B: R.169, E.185 Chain C: R.169, E.185 5 PLIP interactions: 1 interactions with chain A, 2 interactions with chain C, 2 interactions with chain B Metal complexes: A:E.185, C:E.185, C:E.185, B:E.185, B:E.185 MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain A: D.168 Chain B: D.168 Chain C: D.168 Ligands: NA.5 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: A:D.168, C:D.168, B:D.168, H2O.1, H2O.5, H2O.11

2 x NA: SODIUM ION(Non-functional Binders)

NA.5: 7 residues within 4Å: Chain A: D.166, D.168 Chain B: D.166, D.168 Chain C: D.166, D.168 Ligands: MG.11 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.168, B:D.168, B:D.168 NA.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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
A

B
B

C
C

Tetrahydrodipicolinate N-succinyltransferase

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