SMTL ID : 5vo3.1

Crystal structure of DapE in complex with the products (succinic acid and diaminopimelic acid)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x SIN: SUCCINIC ACID(Non-covalent)

SIN.1: 19 residues within 4Å: Chain A: H.71, D.104, E.138, E.139, E.167, P.168, K.179, R.182, G.327, G.328, T.329, S.330, I.352, H.353 Chain B: H.198, Y.201 Ligands: API.2, ZN.3, ZN.4 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.167, A:G.328 Water bridges: A:K.179, A:R.182 Salt bridges: A:K.179, A:R.182, A:H.353, B:H.198 SIN.5: 19 residues within 4Å: Chain A: H.198, Y.201 Chain B: H.71, D.104, E.138, E.139, E.167, P.168, K.179, R.182, G.327, G.328, T.329, S.330, I.352, H.353 Ligands: API.6, ZN.7, ZN.8 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:E.167, B:G.328 Water bridges: B:K.179, B:R.182 Salt bridges: B:K.179, B:R.182, B:H.353, A:H.198

2 x API: 2,6-DIAMINOPIMELIC ACID(Non-covalent)

API.2: 18 residues within 4Å: Chain A: E.138, E.139, A.140, T.141, S.185, T.187, R.262, S.294, G.328, T.329, S.330, R.333, H.353 Chain B: H.198, N.248, N.249 Ligands: SIN.1, ZN.4 18 PLIP interactions: 14 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:E.139, A:S.185, A:T.329, A:T.329, A:T.329, A:T.329, B:N.248, B:N.249 Water bridges: A:A.140, A:A.140, A:T.141, A:T.187, A:R.262, A:R.262, B:N.248 Salt bridges: A:R.262, A:R.262, B:H.198 API.6: 18 residues within 4Å: Chain A: H.198, N.248, N.249 Chain B: E.138, E.139, A.140, T.141, S.185, T.187, R.262, S.294, G.328, T.329, S.330, R.333, H.353 Ligands: SIN.5, ZN.8 18 PLIP interactions: 14 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:E.139, B:S.185, B:T.329, B:T.329, B:T.329, B:T.329, A:N.248, A:N.249 Water bridges: B:A.140, B:A.140, B:T.141, B:T.187, B:R.262, B:R.262, A:N.248 Salt bridges: B:R.262, B:R.262, A:H.198

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 8 residues within 4Å: Chain A: H.71, D.104, M.105, E.138, E.139, E.167 Ligands: SIN.1, ZN.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.71, A:D.104, A:E.167, A:E.167 ZN.4: 8 residues within 4Å: Chain A: V.75, D.104, E.139, H.353 Chain B: H.198 Ligands: SIN.1, API.2, ZN.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.104, A:E.139, A:E.139, A:H.353 ZN.7: 8 residues within 4Å: Chain B: H.71, D.104, M.105, E.138, E.139, E.167 Ligands: SIN.5, ZN.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.71, B:D.104, B:E.167, B:E.167 ZN.8: 8 residues within 4Å: Chain A: H.198 Chain B: V.75, D.104, E.139, H.353 Ligands: SIN.5, API.6, ZN.7 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.104, B:E.139, B:E.139, B:H.353

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nocek, B. et al., Structural Evidence of a Major Conformational Change Triggered by Substrate Binding in DapE Enzymes: Impact on the Catalytic Mechanism. Biochemistry (2018)

Release Date

2018-07-25

Peptides

Succinyl-diaminopimelate desuccinylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Succinyl-diaminopimelate desuccinylase