SMTL ID : 2oz3.1 (2 other biounits)

Crystal structure of L-Rhamnonate dehydratase from Azotobacter vinelandii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-octamer

Ligands

46 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 5 residues within 4Å: Chain A: V.154, R.155, Q.334 Chain C: K.42, Y.43 Ligand excluded by PLIP GOL.2: 4 residues within 4Å: Chain A: G.361, P.363, R.374 Ligands: GOL.3 Ligand excluded by PLIP GOL.3: 5 residues within 4Å: Chain A: P.353, L.359, G.361, E.362 Ligands: GOL.2 Ligand excluded by PLIP GOL.4: 6 residues within 4Å: Chain A: D.108, N.112, L.115, W.276 Chain E: K.42, P.246 Ligand excluded by PLIP GOL.5: 5 residues within 4Å: Chain A: Q.159, W.212, F.338 Chain C: P.186, S.187 Ligand excluded by PLIP GOL.6: 5 residues within 4Å: Chain A: E.283, M.284 Chain E: W.251, M.284 Ligands: GOL.31 Ligand excluded by PLIP GOL.7: 3 residues within 4Å: Chain A: D.69, G.70, N.71 Ligand excluded by PLIP GOL.8: 7 residues within 4Å: Chain A: H.24, I.32, I.36, R.50, T.163, D.216, W.218 Ligand excluded by PLIP GOL.9: 6 residues within 4Å: Chain A: R.234, G.237, L.238, G.263, M.264 Chain C: R.228 Ligand excluded by PLIP GOL.11: 5 residues within 4Å: Chain B: D.108, N.112, R.275, W.276 Chain C: K.42 Ligand excluded by PLIP GOL.12: 5 residues within 4Å: Chain B: V.154, R.155, Q.334 Chain E: K.42, Y.43 Ligand excluded by PLIP GOL.13: 7 residues within 4Å: Chain B: D.222, L.223, N.224 Chain D: D.288, N.314, A.315, L.316 Ligand excluded by PLIP GOL.14: 5 residues within 4Å: Chain B: M.280, E.283, M.284 Chain C: W.251, M.284 Ligand excluded by PLIP GOL.15: 5 residues within 4Å: Chain B: K.42 Chain C: D.108, N.112, R.275, W.276 Ligand excluded by PLIP GOL.16: 7 residues within 4Å: Chain C: Q.159, W.212, P.337, F.338 Chain H: P.186, S.187, G.189 Ligand excluded by PLIP GOL.17: 6 residues within 4Å: Chain C: E.157, E.366, R.369, M.370, R.371, R.374 Ligand excluded by PLIP GOL.18: 7 residues within 4Å: Chain C: E.104, T.301, L.304, K.305 Chain D: L.304, R.333 Ligands: GOL.25 Ligand excluded by PLIP GOL.19: 3 residues within 4Å: Chain C: R.166, M.203, R.206 Ligand excluded by PLIP GOL.20: 5 residues within 4Å: Chain C: I.32, R.50, T.163, D.216, W.218 Ligand excluded by PLIP GOL.22: 6 residues within 4Å: Chain D: W.107, D.108, N.112, R.275, W.276 Chain H: K.42 Ligand excluded by PLIP GOL.23: 5 residues within 4Å: Chain D: K.42, Y.43 Chain G: V.154, R.155, Q.334 Ligand excluded by PLIP GOL.24: 5 residues within 4Å: Chain B: K.42, Y.43 Chain D: V.154, R.155, Q.334 Ligand excluded by PLIP GOL.25: 8 residues within 4Å: Chain C: L.150, G.151, L.304 Chain D: E.104, W.135, L.149, L.304 Ligands: GOL.18 Ligand excluded by PLIP GOL.26: 5 residues within 4Å: Chain E: V.154, R.155, Q.334 Chain G: K.42, Y.43 Ligand excluded by PLIP GOL.27: 4 residues within 4Å: Chain E: G.361, P.363, R.374 Ligands: GOL.28 Ligand excluded by PLIP GOL.28: 5 residues within 4Å: Chain E: P.353, L.359, G.361, E.362 Ligands: GOL.27 Ligand excluded by PLIP GOL.29: 6 residues within 4Å: Chain A: K.42, P.246 Chain E: D.108, N.112, L.115, W.276 Ligand excluded by PLIP GOL.30: 5 residues within 4Å: Chain E: Q.159, W.212, F.338 Chain G: P.186, S.187 Ligand excluded by PLIP GOL.31: 5 residues within 4Å: Chain A: W.251, M.284 Chain E: E.283, M.284 Ligands: GOL.6 Ligand excluded by PLIP GOL.32: 3 residues within 4Å: Chain E: D.69, G.70, N.71 Ligand excluded by PLIP GOL.33: 7 residues within 4Å: Chain E: H.24, I.32, I.36, R.50, T.163, D.216, W.218 Ligand excluded by PLIP GOL.34: 6 residues within 4Å: Chain E: R.234, G.237, L.238, G.263, M.264 Chain G: R.228 Ligand excluded by PLIP GOL.36: 5 residues within 4Å: Chain F: D.108, N.112, R.275, W.276 Chain G: K.42 Ligand excluded by PLIP GOL.37: 5 residues within 4Å: Chain A: K.42, Y.43 Chain F: V.154, R.155, Q.334 Ligand excluded by PLIP GOL.38: 7 residues within 4Å: Chain F: D.222, L.223, N.224 Chain H: D.288, N.314, A.315, L.316 Ligand excluded by PLIP GOL.39: 5 residues within 4Å: Chain F: M.280, E.283, M.284 Chain G: W.251, M.284 Ligand excluded by PLIP GOL.40: 5 residues within 4Å: Chain F: K.42 Chain G: D.108, N.112, R.275, W.276 Ligand excluded by PLIP GOL.41: 7 residues within 4Å: Chain D: P.186, S.187, G.189 Chain G: Q.159, W.212, P.337, F.338 Ligand excluded by PLIP GOL.42: 6 residues within 4Å: Chain G: E.157, E.366, R.369, M.370, R.371, R.374 Ligand excluded by PLIP GOL.43: 7 residues within 4Å: Chain G: E.104, T.301, L.304, K.305 Chain H: L.304, R.333 Ligands: GOL.50 Ligand excluded by PLIP GOL.44: 3 residues within 4Å: Chain G: R.166, M.203, R.206 Ligand excluded by PLIP GOL.45: 5 residues within 4Å: Chain G: I.32, R.50, T.163, D.216, W.218 Ligand excluded by PLIP GOL.47: 6 residues within 4Å: Chain D: K.42 Chain H: W.107, D.108, N.112, R.275, W.276 Ligand excluded by PLIP GOL.48: 5 residues within 4Å: Chain C: V.154, R.155, Q.334 Chain H: K.42, Y.43 Ligand excluded by PLIP GOL.49: 5 residues within 4Å: Chain F: K.42, Y.43 Chain H: V.154, R.155, Q.334 Ligand excluded by PLIP GOL.50: 8 residues within 4Å: Chain G: L.150, G.151, L.304 Chain H: E.104, W.135, L.149, L.304 Ligands: GOL.43 Ligand excluded by PLIP

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

NA.10: 4 residues within 4Å: Chain B: K.179, D.216, E.242, E.270 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.179, B:E.242 NA.21: 4 residues within 4Å: Chain D: K.179, D.216, E.242, E.270 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.179, D:D.216, D:E.242 NA.35: 4 residues within 4Å: Chain F: K.179, D.216, E.242, E.270 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:K.179, F:E.242, F:E.270 Water bridges: F:D.216 NA.46: 4 residues within 4Å: Chain H: K.179, D.216, E.242, E.270 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:K.179, H:K.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Patskovsky, Y. et al., Crystal structure of L-Rhamnonate dehydratase from azotobacter vinelandii. To be Published

Release Date

2007-03-06

Peptides

Mandelate racemase/muconate lactonizing enzyme: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

Mandelate racemase/muconate lactonizing enzyme

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