SMTL ID : 5k8b.1 (1 other biounit)

X-ray structure of KdnA, 8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase, from Shewanella oneidensis in the presence of the external aldimine with PLP and glutamate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

homo-dimer

Ligands

2 x PDG: N-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-D-GLUTAMIC ACID(Non-covalent)(Covalent)

PDG.1: 17 residues within 4Å: Chain A: S.60, G.61, T.62, L.65, F.87, V.131, D.157, C.159, Q.160, S.181, D.183, K.186, G.193, H.325 Chain B: R.222, N.233, R.235 21 PLIP interactions: 15 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:F.87, A:F.87, A:V.131, A:Q.160 Hydrogen bonds: A:G.61, A:T.62, A:T.62, A:Q.160, A:S.181, A:S.181, A:D.183, A:K.186, A:K.186, B:N.233 Salt bridges: A:K.186, A:H.325, B:R.222, B:R.235, B:R.235 Water bridges: B:R.235, B:R.235 PDG.4: 18 residues within 4Å: Chain A: R.222, N.233, R.235 Chain B: S.60, G.61, T.62, T.86, F.87, A.89, V.131, D.157, C.159, Q.160, S.181, D.183, K.186, G.193, H.325 21 PLIP interactions: 14 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:F.87, B:F.87, B:V.131, B:Q.160 Hydrogen bonds: B:G.61, B:T.62, B:Q.160, B:S.181, B:K.186, B:K.186, B:K.186, B:G.193, A:N.233 Salt bridges: B:K.186, B:H.325, A:R.222, A:R.235, A:R.235 Water bridges: A:R.222, A:R.235, A:R.235

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 5 residues within 4Å: Chain A: W.319, N.322, N.323, W.324, H.325 Ligand excluded by PLIP CL.3: 4 residues within 4Å: Chain A: K.262, R.278, F.290, S.292 Ligand excluded by PLIP CL.5: 6 residues within 4Å: Chain B: K.262, R.278, I.280, F.290, L.291, S.292 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zachman-Brockmeyer, T.R. et al., Structures of KdnB and KdnA from Shewanella oneidensis: Key Enzymes in the Formation of 8-Amino-3,8-Dideoxy-d-Manno-Octulosonic Acid. Biochemistry (2016)

Release Date

2016-06-15

Peptides

8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

8-amino-3,8-dideoxy-alpha-D-manno-octulosonate transaminase

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