SMTL ID : 3fsy.1 (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: 9 residues within 4Å: Chain A: E.259, R.292, R.293, N.294, S.295, L.303 Chain B: G.267, R.269, K.279 12 PLIP interactions: 6 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:G.267, B:R.269, B:K.279, A:R.292, A:R.293, A:S.295 Salt bridges: B:R.269, B:R.269, B:K.279, A:R.292, A:R.292 pi-Cation interactions: A:R.292 SCA.3: 21 residues within 4Å: Chain A: R.203, S.205, S.221, I.222, M.223, T.265, G.267, K.279 Chain C: E.201, G.217, G.218, G.243, A.244, V.257, E.259, A.260, L.290, R.292, R.293, N.294, S.295 20 PLIP interactions: 12 interactions with chain C, 8 interactions with chain A Hydrophobic interactions: C:A.244, C:V.257, C:E.259, C:L.290 Hydrogen bonds: C:G.218, C:A.244, C:E.259, C:A.260, C:R.292, C:R.293, C:S.295, A:T.265, A:G.267 pi-Cation interactions: C:R.292 Water bridges: A:S.205, A:S.227, A:G.267, A:R.269 Salt bridges: A:R.203, A:K.279 SCA.9: 7 residues within 4Å: Chain B: E.259, R.292, R.293, N.294, S.295 Chain C: G.267, R.269 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.259, B:R.292, B:R.292, B:N.294, B:S.295 Water bridges: B:E.259 pi-Cation interactions: B:R.292

2 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 B: E.130 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:E.130, A:V.157, A:T.160 Hydrogen bonds: A:T.160, A:T.160 MPD.11: 6 residues within 4Å: Chain B: H.96, R.97, V.157, P.159, T.160 Chain C: E.130 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:E.130, B:V.157, B:T.160 Hydrogen bonds: B:T.160, B:T.160

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

MG.4: 4 residues within 4Å: Chain A: D.168 Chain B: D.168 Chain C: D.168 Ligands: NA.8 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.7, H2O.14 MG.5: 3 residues within 4Å: Chain A: E.185 Chain B: E.185 Chain C: E.185 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:E.185, A:E.185, C:E.185, H2O.6, H2O.12 MG.6: 1 residues within 4Å: Chain A: D.255 No protein-ligand interaction detected (PLIP) MG.7: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

NA.8: 7 residues within 4Å: Chain A: D.166, D.168 Chain B: D.166, D.168 Chain C: D.166, D.168 Ligands: MG.4 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 2 interactions with chain B Hydrogen bonds: A:D.168, B:D.168, B:D.168 Water bridges: C:D.166 NA.13: 1 residues within 4Å: Chain B: D.212 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.212

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

ACY.10: 7 residues within 4Å: Chain A: G.218, A.244 Chain B: R.203, S.205, S.221, I.222, G.224 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Salt bridges: B:R.203 Water bridges: A:G.218, A:G.218 ACY.14: 7 residues within 4Å: Chain B: G.218, A.244 Chain C: R.203, S.205, S.221, I.222, G.224 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Water bridges: B:G.218, C:T.225 Salt bridges: C:R.203

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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