SMTL ID : 4e4f.1

Crystal structure of enolase PC1_0802 (TARGET EFI-502240) from Pectobacterium carotovorum subsp. carotovorum PC1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-octamer

Ligands

24 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 10 residues within 4Å: Chain A: N.59, P.193, E.286, H.336, P.338, D.340, L.413, W.426 Chain D: W.98 Ligands: FMT.6 Ligand excluded by PLIP GOL.3: 8 residues within 4Å: Chain A: P.264, A.265, E.266, N.267, C.270 Chain B: S.327, L.328, Q.330 Ligand excluded by PLIP GOL.5: 6 residues within 4Å: Chain A: T.240, P.264, W.424, N.425 Chain B: Q.330 Chain D: K.94 Ligand excluded by PLIP GOL.7: 9 residues within 4Å: Chain B: N.59, E.286, H.336, P.338, D.340, L.413 Chain C: Y.97, W.98 Ligands: FMT.12 Ligand excluded by PLIP GOL.8: 8 residues within 4Å: Chain B: P.264, A.265, E.266, N.267 Chain C: R.99, W.292 Chain E: L.328, Q.330 Ligand excluded by PLIP GOL.10: 6 residues within 4Å: Chain B: T.240, P.264, W.424, N.425 Chain C: K.94 Chain E: Q.330 Ligand excluded by PLIP GOL.13: 8 residues within 4Å: Chain B: Y.97, W.98 Chain C: N.59, H.336, P.338, D.340, L.413 Ligands: FMT.17 Ligand excluded by PLIP GOL.14: 6 residues within 4Å: Chain B: W.292 Chain C: E.266, N.267, Q.268, A.269, Q.296 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain B: K.94 Chain C: T.240, P.264, W.424, N.425 Chain D: Q.330 Ligand excluded by PLIP GOL.18: 11 residues within 4Å: Chain A: Y.97, W.98 Chain D: N.59, P.193, E.286, H.336, P.338, D.340, L.413, W.426 Ligands: FMT.22 Ligand excluded by PLIP GOL.19: 7 residues within 4Å: Chain D: W.89, Y.93, S.290, I.291, W.292, G.318, R.321 Ligand excluded by PLIP GOL.21: 9 residues within 4Å: Chain A: W.292 Chain D: P.264, A.265, E.266, N.267, C.270 Chain G: S.327, L.328, Q.330 Ligand excluded by PLIP GOL.23: 10 residues within 4Å: Chain E: N.59, P.193, E.286, H.336, P.338, D.340, L.413, W.426 Chain H: W.98 Ligands: FMT.28 Ligand excluded by PLIP GOL.25: 8 residues within 4Å: Chain E: P.264, A.265, E.266, N.267, C.270 Chain F: S.327, L.328, Q.330 Ligand excluded by PLIP GOL.27: 6 residues within 4Å: Chain E: T.240, P.264, W.424, N.425 Chain F: Q.330 Chain H: K.94 Ligand excluded by PLIP GOL.29: 9 residues within 4Å: Chain F: N.59, E.286, H.336, P.338, D.340, L.413 Chain G: Y.97, W.98 Ligands: FMT.34 Ligand excluded by PLIP GOL.30: 8 residues within 4Å: Chain A: L.328, Q.330 Chain F: P.264, A.265, E.266, N.267 Chain G: R.99, W.292 Ligand excluded by PLIP GOL.32: 6 residues within 4Å: Chain A: Q.330 Chain F: T.240, P.264, W.424, N.425 Chain G: K.94 Ligand excluded by PLIP GOL.35: 8 residues within 4Å: Chain F: Y.97, W.98 Chain G: N.59, H.336, P.338, D.340, L.413 Ligands: FMT.39 Ligand excluded by PLIP GOL.36: 6 residues within 4Å: Chain F: W.292 Chain G: E.266, N.267, Q.268, A.269, Q.296 Ligand excluded by PLIP GOL.37: 6 residues within 4Å: Chain F: K.94 Chain G: T.240, P.264, W.424, N.425 Chain H: Q.330 Ligand excluded by PLIP GOL.40: 11 residues within 4Å: Chain E: Y.97, W.98 Chain H: N.59, P.193, E.286, H.336, P.338, D.340, L.413, W.426 Ligands: FMT.44 Ligand excluded by PLIP GOL.41: 7 residues within 4Å: Chain H: W.89, Y.93, S.290, I.291, W.292, G.318, R.321 Ligand excluded by PLIP GOL.43: 9 residues within 4Å: Chain C: S.327, L.328, Q.330 Chain E: W.292 Chain H: P.264, A.265, E.266, N.267, C.270 Ligand excluded by PLIP

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 8 residues within 4Å: Chain A: G.101, P.102, V.103, T.104 Chain D: G.101, P.102, V.103, T.104 Ligand excluded by PLIP CL.9: 8 residues within 4Å: Chain B: G.101, P.102, V.103, T.104 Chain C: G.101, P.102, V.103, T.104 Ligand excluded by PLIP CL.24: 8 residues within 4Å: Chain E: G.101, P.102, V.103, T.104 Chain H: G.101, P.102, V.103, T.104 Ligand excluded by PLIP CL.31: 8 residues within 4Å: Chain F: G.101, P.102, V.103, T.104 Chain G: G.101, P.102, V.103, T.104 Ligand excluded by PLIP

8 x MG: MAGNESIUM ION(Non-covalent)

MG.4: 5 residues within 4Å: Chain A: D.234, E.260, D.261, E.286 Ligands: FMT.6 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.234, A:E.260, A:E.286, H2O.7 MG.11: 5 residues within 4Å: Chain B: D.234, E.260, D.261, E.286 Ligands: FMT.12 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.234, B:E.260, B:E.286, H2O.15 MG.16: 6 residues within 4Å: Chain C: D.234, E.260, D.261, E.286, R.307 Ligands: FMT.17 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.234, C:E.260, C:E.286, H2O.22 MG.20: 5 residues within 4Å: Chain D: D.234, E.260, D.261, E.286 Ligands: FMT.22 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.234, D:E.260, D:E.286, H2O.28 MG.26: 5 residues within 4Å: Chain E: D.234, E.260, D.261, E.286 Ligands: FMT.28 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.234, E:E.260, E:E.286, H2O.35 MG.33: 5 residues within 4Å: Chain F: D.234, E.260, D.261, E.286 Ligands: FMT.34 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.234, F:E.260, F:E.286, H2O.43 MG.38: 6 residues within 4Å: Chain G: D.234, E.260, D.261, E.286, R.307 Ligands: FMT.39 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.234, G:E.260, G:E.286, H2O.50 MG.42: 5 residues within 4Å: Chain H: D.234, E.260, D.261, E.286 Ligands: FMT.44 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.234, H:E.260, H:E.286, H2O.56

8 x FMT: FORMIC ACID(Non-functional Binders)

FMT.6: 9 residues within 4Å: Chain A: D.234, H.236, E.260, E.286, R.307, H.336 Chain D: Y.97 Ligands: GOL.1, MG.4 5 PLIP interactions: 2 interactions with chain D, 3 interactions with chain A Water bridges: D:Y.97, D:Y.97, A:R.169, A:H.236 Hydrogen bonds: A:R.307 FMT.12: 10 residues within 4Å: Chain B: R.169, D.234, H.236, E.260, E.286, R.307, H.336 Chain C: Y.97 Ligands: GOL.7, MG.11 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:R.169, B:R.307, C:Y.97 Water bridges: B:E.260, B:E.260 FMT.17: 11 residues within 4Å: Chain B: Y.97 Chain C: R.169, D.234, H.236, E.260, E.286, R.307, H.336, E.363 Ligands: GOL.13, MG.16 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:R.169, C:R.307, B:Y.97 Water bridges: B:Y.97, B:Y.97 FMT.22: 9 residues within 4Å: Chain A: Y.97 Chain D: D.234, H.236, E.260, E.286, R.307, H.336 Ligands: GOL.18, MG.20 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:R.307, A:Y.97 Water bridges: D:R.169 FMT.28: 9 residues within 4Å: Chain E: D.234, H.236, E.260, E.286, R.307, H.336 Chain H: Y.97 Ligands: GOL.23, MG.26 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain H Hydrogen bonds: E:H.236, E:R.307, H:Y.97 Water bridges: E:D.234 FMT.34: 10 residues within 4Å: Chain F: R.169, D.234, H.236, E.260, E.286, R.307, H.336 Chain G: Y.97 Ligands: GOL.29, MG.33 10 PLIP interactions: 7 interactions with chain F, 3 interactions with chain G Hydrogen bonds: F:R.169, F:H.236, F:R.307 Water bridges: F:D.234, F:E.260, F:E.363, F:E.363, G:Y.97, G:Y.97, G:Y.97 FMT.39: 11 residues within 4Å: Chain F: Y.97 Chain G: R.169, D.234, H.236, E.260, E.286, R.307, H.336, E.363 Ligands: GOL.35, MG.38 7 PLIP interactions: 2 interactions with chain F, 5 interactions with chain G Hydrogen bonds: F:Y.97, F:Y.97, G:R.169, G:H.236, G:R.307 Water bridges: G:E.260, G:E.260 FMT.44: 9 residues within 4Å: Chain E: Y.97 Chain H: D.234, H.236, E.260, E.286, R.307, H.336 Ligands: GOL.40, MG.42 7 PLIP interactions: 4 interactions with chain H, 3 interactions with chain E Hydrogen bonds: H:H.236, H:E.260, H:R.307 Water bridges: H:D.234, E:Y.97, E:Y.97, E:Y.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Patskovsky, Y. et al., Crystal structure of ENOLASE PC1_0802 from Pectobacterium carotovorum. To be Published

Release Date

2012-03-28

Peptides

MANNONATE DEHYDRATASE: 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

MANNONATE DEHYDRATASE