SMTL ID : 3thu.1 (1 other biounit)

Crystal structure of an enolase from sphingomonas sp. ska58 (efi target efi-501683) with bound mg

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-octamer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 7 residues within 4Å: Chain A: D.234, H.236, E.260, D.261, E.286, R.307 Ligands: UNX.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.234, A:E.260, A:E.286, H2O.2, H2O.5 MG.7: 7 residues within 4Å: Chain B: D.234, H.236, E.260, D.261, E.286, R.307 Ligands: UNX.11 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.234, B:E.260, B:E.286, H2O.17, H2O.20 MG.13: 7 residues within 4Å: Chain C: D.234, H.236, E.260, D.261, E.286, R.307 Ligands: UNX.17 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.234, C:E.260, C:E.286, H2O.32, H2O.35 MG.19: 7 residues within 4Å: Chain D: D.234, H.236, E.260, D.261, E.286, R.307 Ligands: UNX.23 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.234, D:E.260, D:E.286, H2O.47, H2O.50 MG.25: 7 residues within 4Å: Chain E: D.234, H.236, E.260, D.261, E.286, R.307 Ligands: UNX.29 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.234, E:E.260, E:E.286, H2O.62, H2O.65 MG.31: 7 residues within 4Å: Chain F: D.234, H.236, E.260, D.261, E.286, R.307 Ligands: UNX.35 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.234, F:E.260, F:E.286, H2O.77, H2O.80 MG.37: 7 residues within 4Å: Chain G: D.234, H.236, E.260, D.261, E.286, R.307 Ligands: UNX.41 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.234, G:E.260, G:E.286, H2O.92, H2O.95 MG.43: 7 residues within 4Å: Chain H: D.234, H.236, E.260, D.261, E.286, R.307 Ligands: UNX.47 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:D.234, H:E.260, H:E.286, H2O.107, H2O.110

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

CL.2: 9 residues within 4Å: Chain A: G.103, P.104, V.105, T.106 Chain F: G.103, P.104, V.105, T.106 Ligands: CL.32 Ligand excluded by PLIP CL.8: 9 residues within 4Å: Chain B: G.103, P.104, V.105, T.106 Chain E: G.103, P.104, V.105, T.106 Ligands: CL.26 Ligand excluded by PLIP CL.14: 9 residues within 4Å: Chain C: G.103, P.104, V.105, T.106 Chain G: G.103, P.104, V.105, T.106 Ligands: CL.38 Ligand excluded by PLIP CL.20: 9 residues within 4Å: Chain D: G.103, P.104, V.105, T.106 Chain H: G.103, P.104, V.105, T.106 Ligands: CL.44 Ligand excluded by PLIP CL.26: 9 residues within 4Å: Chain B: G.103, P.104, V.105, T.106 Chain E: G.103, P.104, V.105, T.106 Ligands: CL.8 Ligand excluded by PLIP CL.32: 9 residues within 4Å: Chain A: G.103, P.104, V.105, T.106 Chain F: G.103, P.104, V.105, T.106 Ligands: CL.2 Ligand excluded by PLIP CL.38: 9 residues within 4Å: Chain C: G.103, P.104, V.105, T.106 Chain G: G.103, P.104, V.105, T.106 Ligands: CL.14 Ligand excluded by PLIP CL.44: 9 residues within 4Å: Chain D: G.103, P.104, V.105, T.106 Chain H: G.103, P.104, V.105, T.106 Ligands: CL.20 Ligand excluded by PLIP

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: R.255, P.256, P.281 Chain C: L.211, E.243, R.246 Ligand excluded by PLIP GOL.4: 11 residues within 4Å: Chain A: N.61, Y.183, H.236, E.286, H.336, A.338, D.340, L.413, W.426 Chain F: Y.99, W.100 Ligand excluded by PLIP GOL.9: 6 residues within 4Å: Chain B: R.255, P.256, P.281 Chain D: L.211, E.243, R.246 Ligand excluded by PLIP GOL.10: 11 residues within 4Å: Chain B: N.61, Y.183, H.236, E.286, H.336, A.338, D.340, L.413, W.426 Chain E: Y.99, W.100 Ligand excluded by PLIP GOL.15: 6 residues within 4Å: Chain B: L.211, E.243, R.246 Chain C: R.255, P.256, P.281 Ligand excluded by PLIP GOL.16: 11 residues within 4Å: Chain C: N.61, Y.183, H.236, E.286, H.336, A.338, D.340, L.413, W.426 Chain G: Y.99, W.100 Ligand excluded by PLIP GOL.21: 6 residues within 4Å: Chain A: L.211, E.243, R.246 Chain D: R.255, P.256, P.281 Ligand excluded by PLIP GOL.22: 11 residues within 4Å: Chain D: N.61, Y.183, H.236, E.286, H.336, A.338, D.340, L.413, W.426 Chain H: Y.99, W.100 Ligand excluded by PLIP GOL.27: 6 residues within 4Å: Chain E: R.255, P.256, P.281 Chain G: L.211, E.243, R.246 Ligand excluded by PLIP GOL.28: 11 residues within 4Å: Chain B: Y.99, W.100 Chain E: N.61, Y.183, H.236, E.286, H.336, A.338, D.340, L.413, W.426 Ligand excluded by PLIP GOL.33: 6 residues within 4Å: Chain F: R.255, P.256, P.281 Chain H: L.211, E.243, R.246 Ligand excluded by PLIP GOL.34: 11 residues within 4Å: Chain A: Y.99, W.100 Chain F: N.61, Y.183, H.236, E.286, H.336, A.338, D.340, L.413, W.426 Ligand excluded by PLIP GOL.39: 6 residues within 4Å: Chain F: L.211, E.243, R.246 Chain G: R.255, P.256, P.281 Ligand excluded by PLIP GOL.40: 11 residues within 4Å: Chain C: Y.99, W.100 Chain G: N.61, Y.183, H.236, E.286, H.336, A.338, D.340, L.413, W.426 Ligand excluded by PLIP GOL.45: 6 residues within 4Å: Chain E: L.211, E.243, R.246 Chain H: R.255, P.256, P.281 Ligand excluded by PLIP GOL.46: 11 residues within 4Å: Chain D: Y.99, W.100 Chain H: N.61, Y.183, H.236, E.286, H.336, A.338, D.340, L.413, W.426 Ligand excluded by PLIP

16 x UNX: UNKNOWN ATOM OR ION(Non-functional Binders)

UNX.5: 9 residues within 4Å: Chain A: R.171, D.234, E.260, E.286, R.307, H.336, E.363 Ligands: MG.1, UNX.6 Ligand excluded by PLIP UNX.6: 7 residues within 4Å: Chain A: R.171, Y.183, H.336, A.338, E.363, M.365 Ligands: UNX.5 Ligand excluded by PLIP UNX.11: 9 residues within 4Å: Chain B: R.171, D.234, E.260, E.286, R.307, H.336, E.363 Ligands: MG.7, UNX.12 Ligand excluded by PLIP UNX.12: 7 residues within 4Å: Chain B: R.171, Y.183, H.336, A.338, E.363, M.365 Ligands: UNX.11 Ligand excluded by PLIP UNX.17: 9 residues within 4Å: Chain C: R.171, D.234, E.260, E.286, R.307, H.336, E.363 Ligands: MG.13, UNX.18 Ligand excluded by PLIP UNX.18: 7 residues within 4Å: Chain C: R.171, Y.183, H.336, A.338, E.363, M.365 Ligands: UNX.17 Ligand excluded by PLIP UNX.23: 9 residues within 4Å: Chain D: R.171, D.234, E.260, E.286, R.307, H.336, E.363 Ligands: MG.19, UNX.24 Ligand excluded by PLIP UNX.24: 7 residues within 4Å: Chain D: R.171, Y.183, H.336, A.338, E.363, M.365 Ligands: UNX.23 Ligand excluded by PLIP UNX.29: 9 residues within 4Å: Chain E: R.171, D.234, E.260, E.286, R.307, H.336, E.363 Ligands: MG.25, UNX.30 Ligand excluded by PLIP UNX.30: 7 residues within 4Å: Chain E: R.171, Y.183, H.336, A.338, E.363, M.365 Ligands: UNX.29 Ligand excluded by PLIP UNX.35: 9 residues within 4Å: Chain F: R.171, D.234, E.260, E.286, R.307, H.336, E.363 Ligands: MG.31, UNX.36 Ligand excluded by PLIP UNX.36: 7 residues within 4Å: Chain F: R.171, Y.183, H.336, A.338, E.363, M.365 Ligands: UNX.35 Ligand excluded by PLIP UNX.41: 9 residues within 4Å: Chain G: R.171, D.234, E.260, E.286, R.307, H.336, E.363 Ligands: MG.37, UNX.42 Ligand excluded by PLIP UNX.42: 7 residues within 4Å: Chain G: R.171, Y.183, H.336, A.338, E.363, M.365 Ligands: UNX.41 Ligand excluded by PLIP UNX.47: 9 residues within 4Å: Chain H: R.171, D.234, E.260, E.286, R.307, H.336, E.363 Ligands: MG.43, UNX.48 Ligand excluded by PLIP UNX.48: 7 residues within 4Å: Chain H: R.171, Y.183, H.336, A.338, E.363, M.365 Ligands: UNX.47 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vetting, M.W. et al., Crystal structure of an enolase from sphingomonas sp. ska58 (efi target efi-501683) with bound mg. to be published

Release Date

2011-09-14

Peptides

Mandelate racemase / muconate lactonizing enzyme family protein: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

G
A

H
A

Mandelate racemase / muconate lactonizing enzyme family protein

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