SMTL ID : 5g0a.1

The crystal structure of a S-selective transaminase from Bacillus megaterium

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

4 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 14 residues within 4Å: Chain A: T.120, G.121, S.122, Y.148, H.149, G.150, E.237, D.269, V.271, L.272, K.298 Chain B: S.329, T.330 Ligands: 1PE.2 14 PLIP interactions: 11 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:E.237, A:V.271, A:K.298 Hydrogen bonds: A:G.121, A:S.122, B:T.330, B:T.330 Water bridges: A:T.120, A:T.120, A:Y.148, A:E.237, B:Y.331 Salt bridges: A:K.298 pi-Stacking: A:Y.148 PLP.7: 13 residues within 4Å: Chain A: S.329, T.330 Chain B: T.120, G.121, S.122, Y.148, H.149, G.150, E.237, D.269, V.271, L.272, K.298 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:V.271, B:K.298 Hydrogen bonds: B:T.120, B:T.120, B:G.121, B:S.122, A:T.330, A:T.330, A:T.330 Water bridges: B:Y.148, B:E.237, A:Y.331 Salt bridges: B:K.298 pi-Stacking: B:Y.148 PLP.12: 13 residues within 4Å: Chain C: T.120, G.121, S.122, Y.148, H.149, G.150, E.237, D.269, V.271, L.272, K.298 Chain D: S.329, T.330 16 PLIP interactions: 4 interactions with chain D, 12 interactions with chain C Hydrogen bonds: D:T.330, D:T.330, D:T.330, C:T.120, C:G.121, C:S.122, C:K.298 Water bridges: D:Y.331, C:T.120, C:T.120, C:Y.148, C:E.237 Hydrophobic interactions: C:V.271, C:K.298 Salt bridges: C:K.298 pi-Stacking: C:Y.148 PLP.18: 13 residues within 4Å: Chain C: S.329, T.330 Chain D: T.120, G.121, S.122, Y.148, H.149, G.150, E.237, D.269, V.271, L.272, K.298 14 PLIP interactions: 11 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:V.271, D:K.298 Hydrogen bonds: D:T.120, D:T.120, D:G.121, D:S.122, D:K.298, C:T.330, C:T.330 Water bridges: D:Y.148, D:E.237, C:Y.331 Salt bridges: D:K.298 pi-Stacking: D:Y.148

4 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.2: 12 residues within 4Å: Chain A: F.56, Q.58, L.59, Y.148, Y.164, A.242, K.298, V.436 Chain B: W.86, T.88, Y.89 Ligands: PLP.1 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.298, B:T.88 1PE.3: 4 residues within 4Å: Chain A: E.428, K.429, D.459, Y.463 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.429, A:D.459 1PE.5: 7 residues within 4Å: Chain A: S.175, F.176, S.177, A.178 Chain B: N.137 Chain C: A.178 Chain D: N.137 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: A:S.175, A:S.177, D:N.137, B:N.137 1PE.19: 11 residues within 4Å: Chain C: W.86, T.88, Y.89 Chain D: F.56, L.59, Y.60, Y.164, A.242, L.272, K.298, V.436 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain C Hydrogen bonds: D:K.298, D:K.298, C:T.88, C:T.88 Water bridges: D:Y.164

4 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 8 residues within 4Å: Chain A: W.111, R.256, K.260, Q.290, P.291, D.292, E.315 Ligands: PGE.6 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.256, A:K.260, A:K.260, A:Q.290, A:D.292, A:E.315 PEG.8: 5 residues within 4Å: Chain A: F.25, S.26, H.410, P.414 Chain B: R.324 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.410 Water bridges: A:Q.420 PEG.10: 7 residues within 4Å: Chain B: W.111, R.256, K.260, Q.290, P.291, D.292, E.315 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.256, B:K.260 Water bridges: B:S.313, B:S.313 PEG.13: 8 residues within 4Å: Chain C: W.111, R.256, K.260, Q.290, P.291, D.292, E.315 Ligands: PG4.16 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:R.256, C:K.260, C:D.292, C:E.315 Water bridges: C:Q.290, C:Q.290

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.6: 7 residues within 4Å: Chain A: Y.135, T.136, R.138, G.263, L.265, E.315 Ligands: PEG.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.315 Water bridges: A:Y.135, A:Y.135, A:R.138, A:R.256, A:K.260, A:D.292 PGE.9: 6 residues within 4Å: Chain B: Y.135, T.136, R.138, G.263, L.265, E.315 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.260, B:K.260 PGE.20: 6 residues within 4Å: Chain D: Y.135, T.136, R.138, G.263, L.265, E.315 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.260 Water bridges: D:E.315

5 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.11: 7 residues within 4Å: Chain A: W.86, T.88, Y.89 Chain B: V.34, F.56, L.59, V.436 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.88 PG4.14: 5 residues within 4Å: Chain A: N.137 Chain B: S.177, A.178 Chain C: N.137 Chain D: A.178 3 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: C:N.137, B:S.177, A:N.137 PG4.15: 7 residues within 4Å: Chain C: F.56, L.59, Y.164, V.436 Chain D: W.86, T.88, Y.89 1 PLIP interactions: 1 interactions with chain C Water bridges: C:K.298 PG4.16: 7 residues within 4Å: Chain C: Y.135, T.136, R.138, G.263, L.265, E.315 Ligands: PEG.13 3 PLIP interactions: 3 interactions with chain C Water bridges: C:Y.135, C:Y.135, C:K.260 PG4.17: 4 residues within 4Å: Chain C: E.428, K.429, D.459, Y.463 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.429, C:D.459

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Van Oosterwijk, N. et al., Structural Basis of Substrate Range and Enantioselectivity of Two S-Selective Omega- Transaminases. Biochemistry (2016)

Release Date

2016-07-27

Peptides

TRANSAMINASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

TRANSAMINASE

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