SMTL ID : 5g09.1

The crystal structure of a S-selective transaminase from Bacillus megaterium bound with R-alpha-methylbenzylamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-tetramer

Ligands

4 x 6DF: [6-methyl-5-oxidanyl-4-[(~{E})-[(1~{R})-1-phenylethyl]iminomethyl]pyridin-3-yl]methyl dihydrogen phosphate(Non-covalent)

6DF.1: 17 residues within 4Å: Chain A: L.59, Y.60, T.120, G.121, S.122, Y.148, H.149, G.150, E.237, A.242, D.269, V.271, L.272, K.298 Chain B: V.328, S.329, T.330 18 PLIP interactions: 14 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:L.59, A:Y.60, A:Y.148, A:A.242, A:V.271, A:L.272, B:V.328 Hydrogen bonds: A:G.121, A:S.122, A:W.151, A:K.298, B:T.330, B:T.330 Water bridges: A:T.120, A:S.122, A:Y.148, A:E.237, B:Y.331 6DF.6: 19 residues within 4Å: Chain A: V.328, S.329, T.330 Chain B: L.59, Y.60, T.120, G.121, S.122, Y.148, H.149, G.150, Y.164, E.237, A.242, D.269, V.271, L.272, K.298, V.436 21 PLIP interactions: 17 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.59, B:Y.60, B:Y.148, B:Y.164, B:A.242, B:V.271, B:L.272, B:V.436, A:V.328 Hydrogen bonds: B:T.120, B:G.121, B:S.122, B:W.151, B:K.298, A:T.330 Water bridges: B:T.120, B:Y.148, B:Y.148, B:E.237, A:S.329, A:Y.331 6DF.9: 17 residues within 4Å: Chain C: L.59, Y.60, T.120, G.121, S.122, Y.148, H.149, G.150, W.151, E.237, A.242, D.269, V.271, L.272, K.298 Chain D: S.329, T.330 17 PLIP interactions: 14 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:L.59, C:Y.60, C:Y.148, C:A.242, C:V.271, C:L.272 Hydrogen bonds: C:G.121, C:S.122, C:W.151, C:K.298, D:T.330, D:T.330 Water bridges: C:T.120, C:S.122, C:Y.148, C:E.237, D:Y.331 6DF.14: 17 residues within 4Å: Chain C: S.329, T.330 Chain D: L.59, Y.60, T.120, G.121, S.122, Y.148, H.149, G.150, E.237, A.242, D.269, V.271, L.272, K.298, V.436 20 PLIP interactions: 17 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:L.59, D:Y.60, D:Y.148, D:A.242, D:V.271, D:L.272, D:V.436 Hydrogen bonds: D:T.120, D:G.121, D:S.122, D:W.151, D:K.298, C:T.330 Water bridges: D:T.120, D:Y.148, D:Y.148, D:E.237, C:S.329, C:Y.331 Salt bridges: D:K.298

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

PGE.2: 6 residues within 4Å: Chain A: Y.135, T.136, R.138, G.263, L.265, E.315 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.315 Water bridges: A:Y.135, A:Y.135, A:K.260 PGE.3: 3 residues within 4Å: Chain A: N.137 Chain B: S.177 Chain C: N.137 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:N.137, B:S.177 PGE.5: 7 residues within 4Å: Chain A: F.56, L.59, Y.164, V.436 Chain B: W.86, T.88, Y.89 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.164, B:T.88 Water bridges: A:Y.164 PGE.7: 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 Hydrogen bonds: B:E.315 Water bridges: B:K.260 PGE.8: 6 residues within 4Å: Chain A: W.86, T.88, Y.89 Chain B: F.56, L.59, V.436 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:T.88 Water bridges: B:Y.164, B:Y.164 PGE.10: 6 residues within 4Å: Chain C: Y.135, T.136, R.138, G.263, L.265, E.315 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.315 Water bridges: C:Y.135, C:Y.135 PGE.11: 6 residues within 4Å: Chain C: W.86, T.88, Y.89 Chain D: F.56, L.59, V.436 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Water bridges: D:Y.164, D:Y.164 Hydrogen bonds: C:T.88 PGE.12: 3 residues within 4Å: Chain C: E.428, K.429, Y.463 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.429

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

1PE.4: 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

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

PG4.13: 9 residues within 4Å: Chain C: F.25, V.34, F.56, L.59, Y.164, V.436 Chain D: W.86, T.88, Y.89 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain C Water bridges: D:T.88, D:T.88, C:Y.164, C:Y.164, C:Y.164 PG4.16: 5 residues within 4Å: Chain A: S.177, A.178 Chain B: N.137 Chain C: A.178 Chain D: N.137 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:N.137, B:N.137

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

PEG.15: 5 residues within 4Å: Chain D: Y.135, T.136, R.138, G.263, L.265 No protein-ligand interaction detected (PLIP)

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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