SMTL ID : 3g0t.1

Crystal structure of putative aspartate aminotransferase (NP_905498.1) from Porphyromonas gingivalis W83 at 1.75 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: H.235, E.238, L.240 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.233, A:H.235 NA.13: 4 residues within 4Å: Chain B: H.235, E.238, P.239, L.240 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.235, B:H.235 Water bridges: B:L.240

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

CL.2: 2 residues within 4Å: Chain A: L.148, R.151 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: K.147, L.148, R.151 Ligand excluded by PLIP

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

EDO.3: 4 residues within 4Å: Chain A: W.317, A.320, A.321, K.324 Ligand excluded by PLIP EDO.4: 5 residues within 4Å: Chain A: S.76, I.77 Chain B: P.54, L.56, P.57 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: D.250, N.251, K.277, L.278, R.281 Ligand excluded by PLIP EDO.6: 3 residues within 4Å: Chain A: F.163, D.361 Ligands: EDO.12 Ligand excluded by PLIP EDO.7: 8 residues within 4Å: Chain A: N.126, H.129, R.132, E.133, Y.134, G.135, Q.155, C.184 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: G.55, L.56, Y.340, K.343, S.416 Ligand excluded by PLIP EDO.9: 6 residues within 4Å: Chain A: P.54, G.55, L.56, P.57 Chain B: S.76, I.77 Ligand excluded by PLIP EDO.10: 2 residues within 4Å: Chain A: N.247, Y.248 Ligand excluded by PLIP EDO.11: 3 residues within 4Å: Chain A: P.236, D.328, G.329 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: F.163, Q.197, Y.360, D.361, K.362 Ligands: EDO.6 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain B: D.250, N.251, K.277, L.278, R.281 Ligand excluded by PLIP EDO.18: 5 residues within 4Å: Chain B: S.234, H.235, P.236, G.329, N.332 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain B: I.28, E.50, M.51, G.52, R.412 Ligand excluded by PLIP EDO.20: 7 residues within 4Å: Chain B: N.126, R.132, E.133, Y.134, G.135, Q.155, C.184 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain B: W.317, A.320, A.321, K.324 Ligand excluded by PLIP EDO.22: 2 residues within 4Å: Chain B: N.247, Y.248 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: F.163, Q.197, Y.360, D.361, K.362 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain A: G.291 Chain B: R.151 Ligand excluded by PLIP EDO.25: 4 residues within 4Å: Chain B: Y.134, Y.177, T.180, F.183 Ligand excluded by PLIP

2 x PE4: 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL(Non-functional Binders)

PE4.15: 4 residues within 4Å: Chain B: Q.60, I.61, E.64, T.65 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.64 PE4.16: 6 residues within 4Å: Chain B: S.92, D.102, I.103, P.104, G.276, K.277 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:K.277 Water bridges: B:S.92, B:I.103, B:A.105, B:G.276, B:G.276

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fleischman, N.M. et al., Molecular characterization of novel pyridoxal-5'-phosphate-dependent enzymes from the human microbiome. Protein Sci. (2014)

Release Date

2009-02-10

Peptides

Putative aminotransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative aminotransferase