SMTL ID : 8onm.1

Crystal structure of D-amino acid aminotransferase from Aminobacterium colombiense point mutant E113A complexed with D-glutamate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: A.130, L.131, H.132, S.158, A.161, R.246, G.248 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.132, A:R.246, A:G.248 EDO.6: 4 residues within 4Å: Chain B: M.46, Q.203, E.207, W.275 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.203, B:E.207 Water bridges: B:E.207 EDO.7: 4 residues within 4Å: Chain B: V.245, R.246, I.251, G.255 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.246 EDO.8: 3 residues within 4Å: Chain B: I.214, Q.215, V.216 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.216

4 x NO3: NITRATE ION(Non-functional Binders)

NO3.2: 8 residues within 4Å: Chain A: F.34, T.36, R.90, K.144, Y.148, H.177 Chain B: R.29 Ligands: PMP.4 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.90, A:K.144, A:K.144, B:R.29, B:R.29 NO3.3: 6 residues within 4Å: Chain A: H.177, G.236, T.237, V.238, K.239 Ligands: PMP.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.236, A:T.237, A:V.238, A:K.239 Water bridges: A:K.239 NO3.10: 6 residues within 4Å: Chain B: H.177, G.236, T.237, V.238, K.239 Ligands: PW0.5 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.236, B:V.238, B:K.239 Water bridges: B:T.36, B:K.239 NO3.11: 9 residues within 4Å: Chain A: R.29 Chain B: F.34, T.36, R.90, K.144, Y.148, H.177 Ligands: PW0.5, PMP.9 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.36, B:T.36, B:R.90, B:K.144, A:R.29, A:R.29 Water bridges: B:T.36

2 x PMP: 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PMP.4: 20 residues within 4Å: Chain A: H.50, R.53, R.138, K.144, Y.148, E.174, G.175, S.176, H.177, S.178, T.179, L.197, G.199, T.200, T.201, T.235, G.236, T.237 Ligands: NO3.2, NO3.3 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:L.197 Hydrogen bonds: A:K.144, A:Y.148, A:Y.148, A:H.177, A:T.200, A:T.200, A:T.201, A:T.201, A:T.237 Water bridges: A:R.53, A:R.53, A:R.90, A:T.179, A:R.202 Salt bridges: A:H.50, A:R.53 PMP.9: 20 residues within 4Å: Chain B: H.50, R.53, R.138, K.144, Y.148, E.174, G.175, S.176, H.177, S.178, T.179, L.197, G.199, T.200, T.201, T.235, G.236, T.237 Ligands: PW0.5, NO3.11 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:L.197 Hydrogen bonds: B:K.144, B:Y.148, B:E.174, B:H.177, B:T.200, B:T.201, B:T.237 Water bridges: B:T.36, B:R.53, B:T.179, B:R.202 Salt bridges: B:H.50, B:R.53

1 x PW0: (~{Z})-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]pent-2-enedioic acid(Non-covalent)

PW0.5: 27 residues within 4Å: Chain A: R.29 Chain B: F.34, T.36, H.50, R.53, R.90, R.138, K.144, Y.148, E.174, G.175, S.176, H.177, S.178, T.179, L.197, G.199, T.200, T.201, T.235, G.236, T.237, V.238, K.239 Ligands: PMP.9, NO3.10, NO3.11 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.36, B:T.36, B:K.144, B:Y.148, B:T.200, B:T.200, B:T.201, B:T.237, B:V.238, B:K.239 Water bridges: B:R.53, B:R.53, B:R.90, B:T.179 Salt bridges: B:H.50, B:R.53, B:R.90, B:K.144, B:H.177, B:K.239, A:R.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shilova, S.A. et al., Probing of the structural and catalytic roles of the residues in the active site of transaminase from Aminobacterium colombiense. To Be Published

Release Date

2024-04-10

Peptides

Aminotransferase class IV: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Aminotransferase class IV

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