SMTL ID : 4dyj.1

Crystal structure of a broad specificity amino acid racemase (Bar) within internal aldimine linkage

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

14 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: A.390, L.391 Chain B: R.326, K.346 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Water bridges: B:R.326 Salt bridges: B:R.326, B:K.346 Hydrogen bonds: A:L.391 SO4.2: 4 residues within 4Å: Chain A: R.326, K.346 Chain B: A.390, L.391 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.326, A:K.346 Hydrogen bonds: B:L.391 SO4.3: 2 residues within 4Å: Chain A: V.408, D.409 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.409 SO4.4: 4 residues within 4Å: Chain A: R.340, G.376, G.377, E.378 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.378 Salt bridges: A:R.340 SO4.5: 3 residues within 4Å: Chain A: W.227, K.230, H.231 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.230, A:H.231 SO4.6: 2 residues within 4Å: Chain A: Q.374, A.375 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.375 SO4.7: 5 residues within 4Å: Chain A: M.179, A.180, T.181, W.182, R.185 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.180 Water bridges: A:R.185 Salt bridges: A:R.185 SO4.9: 2 residues within 4Å: Chain B: V.408, D.409 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.409 SO4.10: 5 residues within 4Å: Chain B: L.335, R.340, G.376, G.377, E.378 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.378 Salt bridges: B:R.340 SO4.11: 2 residues within 4Å: Chain B: H.333, P.342 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.333 SO4.12: 3 residues within 4Å: Chain B: K.373, Q.374, A.375 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.375 SO4.13: 3 residues within 4Å: Chain B: T.181, W.182, S.183 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.182, B:S.183 SO4.14: 3 residues within 4Å: Chain B: H.339, R.340, F.359 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.340 Salt bridges: B:H.339 SO4.15: 2 residues within 4Å: Chain B: K.211, R.215 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.211, B:R.215

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.8: 7 residues within 4Å: Chain A: Y.301, S.348, M.349, N.350, T.351 Chain B: K.75, R.174 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:Y.301, A:Y.301, A:M.349, A:N.350, A:N.350, A:T.351, B:R.174, B:R.174 Water bridges: A:Y.320 GOL.16: 8 residues within 4Å: Chain A: K.75, R.174 Chain B: Y.301, Y.320, S.348, M.349, N.350, T.351 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Y.301, B:Y.301, B:Y.320, B:M.349, B:N.350, B:T.351, B:T.351 Water bridges: B:T.351

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wu, H.M. et al., Crystal structures of lysine-preferred racemases, the non-antibiotic selectable markers for transgenic plants. Plos One (2012)

Release Date

2013-03-06

Peptides

broad specificity amino acid racemase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

broad specificity amino acid racemase

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