SMTL ID : 1kgq.1

Crystal Structure of Tetrahydrodipicolinate N-Succinyltransferase in Complex with L-2-aminopimelate and Succinamide-CoA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-trimer

Ligands

3 x NPI: (2S)-2-AMINOHEPTANEDIOIC ACID(Non-covalent)

NPI.1: 15 residues within 4Å: Chain A: R.104, V.122, M.124, M.139, D.141, L.270 Chain C: F.67, R.112, N.129, S.148, G.166, V.167, L.168, E.169 Ligands: SCO.2 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain C Hydrogen bonds: A:D.141, C:N.129, C:S.148, C:V.167, C:L.168, C:E.169 Water bridges: A:D.141 Salt bridges: A:R.104, C:R.112 NPI.3: 15 residues within 4Å: Chain A: F.67, R.112, N.129, S.148, G.166, V.167, L.168, E.169 Chain B: R.104, V.122, M.124, M.139, D.141, L.270 Ligands: SCO.4 9 PLIP interactions: 6 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.129, A:S.148, A:V.167, A:L.168, A:E.169, B:D.141 Salt bridges: A:R.112, B:R.104 Water bridges: B:D.141 NPI.5: 15 residues within 4Å: Chain B: F.67, R.112, N.129, S.148, G.166, V.167, L.168, E.169 Chain C: R.104, V.122, M.124, M.139, D.141, L.270 Ligands: SCO.6 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain C Hydrogen bonds: B:N.129, B:S.148, B:V.167, B:L.168, B:E.169, C:D.141 Salt bridges: B:R.112, C:R.104 Water bridges: C:D.141

3 x SCO: SUCCINAMIDE-COA(Non-covalent)

SCO.2: 26 residues within 4Å: Chain A: S.159, G.160, F.183, G.185, A.186, R.187, S.203, M.204, R.217, V.234, V.253, K.254, K.259, T.260, K.263 Chain C: T.145, G.163, G.165, G.166, E.189, V.191, E.192, S.211, R.213, Y.248 Ligands: NPI.1 31 PLIP interactions: 16 interactions with chain A, 15 interactions with chain C Hydrogen bonds: A:S.159, A:A.186, A:S.203, A:M.204, C:G.166, C:E.189, C:E.192, C:S.211, C:S.211, C:S.211, C:R.213 Water bridges: A:D.141, A:T.142, A:R.187, A:R.217, C:T.145, C:G.166, C:E.169, C:E.192, C:S.211, C:S.211, C:S.211, C:T.212 Salt bridges: A:R.187, A:R.217, A:K.254, A:K.254, A:K.259, A:K.259, A:K.263, A:K.263 SCO.4: 26 residues within 4Å: Chain A: T.145, G.163, G.165, G.166, E.189, V.191, E.192, S.211, R.213, Y.248 Chain B: S.159, G.160, F.183, G.185, A.186, R.187, S.203, M.204, R.217, V.234, V.253, K.254, K.259, T.260, K.263 Ligands: NPI.3 31 PLIP interactions: 15 interactions with chain A, 16 interactions with chain B Hydrogen bonds: A:G.166, A:E.189, A:E.192, A:S.211, A:S.211, A:S.211, A:R.213, B:S.159, B:A.186, B:S.203, B:M.204 Water bridges: A:T.145, A:G.166, A:E.169, A:E.192, A:S.211, A:S.211, A:S.211, A:T.212, B:D.141, B:T.142, B:R.187, B:R.217 Salt bridges: B:R.187, B:R.217, B:K.254, B:K.254, B:K.259, B:K.259, B:K.263, B:K.263 SCO.6: 26 residues within 4Å: Chain B: T.145, G.163, G.165, G.166, E.189, V.191, E.192, S.211, R.213, Y.248 Chain C: S.159, G.160, F.183, G.185, A.186, R.187, S.203, M.204, R.217, V.234, V.253, K.254, K.259, T.260, K.263 Ligands: NPI.5 31 PLIP interactions: 16 interactions with chain C, 15 interactions with chain B Hydrogen bonds: C:S.159, C:A.186, C:S.203, C:M.204, B:G.166, B:E.189, B:E.192, B:S.211, B:S.211, B:S.211, B:R.213 Water bridges: C:D.141, C:T.142, C:R.187, C:R.217, B:T.145, B:G.166, B:E.169, B:E.192, B:S.211, B:S.211, B:S.211, B:T.212 Salt bridges: C:R.187, C:R.217, C:K.254, C:K.254, C:K.259, C:K.259, C:K.263, C:K.263

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Beaman, T.W. et al., Acyl group specificity at the active site of tetrahydridipicolinate N-succinyltransferase. Protein Sci. (2002)

Release Date

2002-04-03

Peptides

2,3,4,5-TETRAHYDROPYRIDINE-2-CARBOXYLATE N-SUCCINYLTRANSFERASE: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

2,3,4,5-TETRAHYDROPYRIDINE-2-CARBOXYLATE N-SUCCINYLTRANSFERASE

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