SMTL ID : 4itb.1

Structure of bacterial enzyme in complex with cofactor and substrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 26 residues within 4Å: Chain A: V.129, M.130, P.131, W.132, N.133, Q.138, K.156, H.157, A.158, S.159, A.189, V.192, T.207, G.208, S.209, A.212, S.215, E.230, L.231, G.232, C.264, I.311, E.361, F.363 Ligands: SSN.2, EDO.6 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:P.131, A:F.363, A:F.363 Hydrogen bonds: A:M.130, A:N.133, A:Q.138, A:S.159, A:A.189, A:G.208, A:S.209, A:S.209, A:S.215, A:S.215, A:E.230, A:E.361 Water bridges: A:W.132, A:S.159, A:S.159, A:N.160 Salt bridges: A:K.156 NDP.16: 25 residues within 4Å: Chain B: V.129, M.130, P.131, W.132, N.133, Q.138, K.156, H.157, A.158, S.159, A.189, V.192, T.207, G.208, S.209, A.212, S.215, E.230, L.231, G.232, C.264, I.311, E.361, F.363 Ligands: SSN.17 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:P.131, B:F.363, B:F.363 Hydrogen bonds: B:M.130, B:N.133, B:Q.138, B:S.159, B:A.189, B:G.208, B:S.209, B:S.209, B:S.215, B:S.215, B:E.230 Water bridges: B:W.132, B:S.159, B:S.159, B:N.160, B:E.361 Salt bridges: B:K.156

2 x SSN: 4-OXOBUTANOIC ACID(Covalent)

SSN.2: 11 residues within 4Å: Chain A: N.133, F.134, W.137, Q.138, R.141, E.230, S.263, C.264, I.265, S.421 Ligands: NDP.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.134 Hydrogen bonds: A:N.133, A:Q.138, A:C.264, A:S.421 Water bridges: A:K.88, A:K.88, A:S.421 Salt bridges: A:K.88, A:R.141 SSN.17: 11 residues within 4Å: Chain B: N.133, F.134, W.137, Q.138, R.141, E.230, S.263, C.264, I.265, S.421 Ligands: NDP.16 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.134, B:I.265 Hydrogen bonds: B:N.133, B:Q.138, B:C.264, B:S.421 Water bridges: B:K.88, B:K.88, B:S.421 Salt bridges: B:K.88, B:R.141

24 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 7 residues within 4Å: Chain A: E.169, E.173, F.177, P.178, G.180, V.181, F.182 Ligand excluded by PLIP EDO.4: 11 residues within 4Å: Chain A: L.126, P.145, A.146, A.149, N.151, G.443, I.444, R.445, T.446, F.447, V.448 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: P.24, S.190, Q.191 Ligands: EDO.11 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: D.314, I.315, Q.318, E.361, L.362, F.363 Ligands: NDP.1 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: K.33, E.36, A.37, E.179 Ligand excluded by PLIP EDO.8: 7 residues within 4Å: Chain A: P.226, T.227, Y.435 Chain B: P.226, T.227, Y.435 Ligands: EDO.9 Ligand excluded by PLIP EDO.9: 10 residues within 4Å: Chain A: A.217, A.220, G.221, K.225, T.227, Y.435 Chain B: G.221, T.227, Y.435 Ligands: EDO.8 Ligand excluded by PLIP EDO.10: 8 residues within 4Å: Chain A: G.208, S.209, E.210, P.211, L.231, G.232, E.361, F.387 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: P.24, Q.194 Ligands: EDO.5 Ligand excluded by PLIP EDO.12: 1 residues within 4Å: Chain A: Q.222 Ligand excluded by PLIP EDO.13: 9 residues within 4Å: Chain A: G.411, A.412, P.426, F.427, G.428, R.437 Chain B: A.450, K.451, T.452 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: D.409, A.410, T.430, K.431 Chain B: L.123, N.449 Ligand excluded by PLIP EDO.15: 10 residues within 4Å: Chain A: I.5, K.156, H.157, A.158, S.159, P.162, A.165, L.185, L.186, I.187 Ligand excluded by PLIP EDO.18: 7 residues within 4Å: Chain B: E.169, E.173, F.177, P.178, G.180, V.181, F.182 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain B: P.24, Q.194 Ligands: EDO.21 Ligand excluded by PLIP EDO.20: 3 residues within 4Å: Chain B: S.290, L.291, D.302 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain B: P.24, S.190, Q.191 Ligands: EDO.19 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain A: L.123, N.449 Chain B: D.409, A.410, T.430, K.431 Ligand excluded by PLIP EDO.23: 11 residues within 4Å: Chain B: L.126, P.145, A.146, A.149, N.151, G.443, I.444, R.445, T.446, F.447, V.448 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain B: R.42, F.46, R.49, L.104, Y.120, P.122, A.149 Ligand excluded by PLIP EDO.25: 6 residues within 4Å: Chain B: S.209, E.210, P.211, L.231, E.361, F.387 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain A: L.441, R.445 Chain B: L.441, A.442, R.445 Ligand excluded by PLIP EDO.27: 2 residues within 4Å: Chain A: P.211 Chain B: Q.222 Ligand excluded by PLIP EDO.28: 9 residues within 4Å: Chain A: A.450, K.451, T.452 Chain B: G.411, A.412, P.426, F.427, G.428, R.437 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Park, J. et al., Structural Basis for a Cofactor-dependent Oxidation Protection and Catalysis of Cyanobacterial Succinic Semialdehyde Dehydrogenase. J.Biol.Chem. (2013)

Release Date

2013-04-24

Peptides

Succinate-semialdehyde dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Succinate-semialdehyde dehydrogenase

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