SMTL ID : 3t6c.1

Crystal structure of an enolase from pantoea ananatis (efi target efi-501676) with bound d-gluconate and mg

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-octamer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.246, E.272, E.298, R.319 Ligands: GCO.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.246, A:E.272, A:E.298, H2O.1 MG.9: 5 residues within 4Å: Chain B: D.246, E.272, E.298, R.319 Ligands: GCO.10 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.246, B:E.272, B:E.298, H2O.19 MG.17: 5 residues within 4Å: Chain C: D.246, E.272, E.298, R.319 Ligands: GCO.18 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.246, C:E.272, C:E.298, H2O.37 MG.25: 5 residues within 4Å: Chain D: D.246, E.272, E.298, R.319 Ligands: GCO.26 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.246, D:E.272, D:E.298, H2O.56 MG.33: 5 residues within 4Å: Chain E: D.246, E.272, E.298, R.319 Ligands: GCO.34 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.246, E:E.272, E:E.298, H2O.74 MG.41: 5 residues within 4Å: Chain F: D.246, E.272, E.298, R.319 Ligands: GCO.42 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.246, F:E.272, F:E.298, H2O.92 MG.49: 5 residues within 4Å: Chain G: D.246, E.272, E.298, R.319 Ligands: GCO.50 4 PLIP interactions: 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.246, G:E.272, G:E.298, H2O.111 MG.57: 5 residues within 4Å: Chain H: D.246, E.272, E.298, R.319 Ligands: GCO.58 4 PLIP interactions: 3 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.246, H:E.272, H:E.298, H2O.129

8 x GCO: D-gluconic acid(Non-covalent)

GCO.2: 17 residues within 4Å: Chain A: Q.66, R.175, Y.181, L.191, D.246, H.248, E.272, E.298, R.319, H.348, P.350, D.352, E.375, W.427 Chain B: Y.103, W.104 Ligands: MG.1 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:Q.66, A:Y.181, A:Y.181, A:H.248, A:E.298, A:E.298 Water bridges: A:Y.148, A:Y.148, A:D.352, A:D.352 Salt bridges: A:H.150, A:R.175, A:R.319, A:H.348 GCO.10: 16 residues within 4Å: Chain A: Y.103, W.104 Chain B: Q.66, H.150, R.175, D.246, H.248, E.272, E.298, R.319, H.348, P.350, D.352, E.375, W.427 Ligands: MG.9 11 PLIP interactions: 10 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.66, B:R.175, B:H.248, B:E.298, B:E.298 Water bridges: B:R.175, A:Y.103 Salt bridges: B:H.150, B:R.175, B:R.319, B:H.348 GCO.18: 17 residues within 4Å: Chain C: Q.66, R.175, Y.181, L.191, D.246, H.248, E.272, E.298, R.319, H.348, P.350, D.352, E.375, W.427 Chain D: Y.103, W.104 Ligands: MG.17 14 PLIP interactions: 14 interactions with chain C Hydrogen bonds: C:Q.66, C:Y.181, C:Y.181, C:H.248, C:E.298, C:E.298 Water bridges: C:Y.148, C:Y.148, C:D.352, C:D.352 Salt bridges: C:H.150, C:R.175, C:R.319, C:H.348 GCO.26: 16 residues within 4Å: Chain C: Y.103, W.104 Chain D: Q.66, H.150, R.175, D.246, H.248, E.272, E.298, R.319, H.348, P.350, D.352, E.375, W.427 Ligands: MG.25 11 PLIP interactions: 10 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:Q.66, D:R.175, D:H.248, D:E.298, D:E.298 Water bridges: D:R.175, C:Y.103 Salt bridges: D:H.150, D:R.175, D:R.319, D:H.348 GCO.34: 17 residues within 4Å: Chain E: Q.66, R.175, Y.181, L.191, D.246, H.248, E.272, E.298, R.319, H.348, P.350, D.352, E.375, W.427 Chain F: Y.103, W.104 Ligands: MG.33 15 PLIP interactions: 15 interactions with chain E Hydrogen bonds: E:Q.66, E:Y.181, E:Y.181, E:D.246, E:H.248, E:E.298 Water bridges: E:Y.148, E:Y.148, E:E.272, E:D.352, E:D.352 Salt bridges: E:H.150, E:R.175, E:R.319, E:H.348 GCO.42: 16 residues within 4Å: Chain E: Y.103, W.104 Chain F: Q.66, H.150, R.175, D.246, H.248, E.272, E.298, R.319, H.348, P.350, D.352, E.375, W.427 Ligands: MG.41 11 PLIP interactions: 10 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:Q.66, F:R.175, F:H.248, F:E.298, F:E.298 Water bridges: F:R.175, E:Y.103 Salt bridges: F:H.150, F:R.175, F:R.319, F:H.348 GCO.50: 17 residues within 4Å: Chain G: Q.66, R.175, Y.181, L.191, D.246, H.248, E.272, E.298, R.319, H.348, P.350, D.352, E.375, W.427 Chain H: Y.103, W.104 Ligands: MG.49 14 PLIP interactions: 14 interactions with chain G Hydrogen bonds: G:Q.66, G:Y.181, G:Y.181, G:H.248, G:E.298, G:E.298 Water bridges: G:Y.148, G:Y.148, G:D.352, G:D.352 Salt bridges: G:H.150, G:R.175, G:R.319, G:H.348 GCO.58: 16 residues within 4Å: Chain G: Y.103, W.104 Chain H: Q.66, H.150, R.175, D.246, H.248, E.272, E.298, R.319, H.348, P.350, D.352, E.375, W.427 Ligands: MG.57 11 PLIP interactions: 1 interactions with chain G, 10 interactions with chain H Water bridges: G:Y.103, H:R.175 Hydrogen bonds: H:Q.66, H:R.175, H:H.248, H:E.298, H:E.298 Salt bridges: H:H.150, H:R.175, H:R.319, H:H.348

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

CL.3: 8 residues within 4Å: Chain A: G.107, P.108, V.109, M.110 Chain B: G.107, P.108, V.109, M.110 Ligand excluded by PLIP CL.19: 8 residues within 4Å: Chain C: G.107, P.108, V.109, M.110 Chain D: G.107, P.108, V.109, M.110 Ligand excluded by PLIP CL.35: 8 residues within 4Å: Chain E: G.107, P.108, V.109, M.110 Chain F: G.107, P.108, V.109, M.110 Ligand excluded by PLIP CL.51: 8 residues within 4Å: Chain G: G.107, P.108, V.109, M.110 Chain H: G.107, P.108, V.109, M.110 Ligand excluded by PLIP

36 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 5 residues within 4Å: Chain A: E.278, R.439 Chain B: A.99, V.100 Ligands: EDO.11 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: G.182, G.183, A.184, K.198, I.202, F.217, D.218 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: P.253, N.279, R.439 Chain E: G.342, R.344, N.370 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: W.95, W.306, P.330, K.333 Chain H: L.340 Ligand excluded by PLIP EDO.11: 6 residues within 4Å: Chain B: W.95, R.105, N.106, N.111, V.301 Ligands: EDO.4 Ligand excluded by PLIP EDO.12: 5 residues within 4Å: Chain B: W.95, W.306, P.330, K.333 Chain E: L.340 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: A.99, V.100 Chain B: E.278, R.439 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain B: P.253, N.279, R.439 Chain H: G.342, R.344, N.370 Ligand excluded by PLIP EDO.15: 8 residues within 4Å: Chain B: P.350, G.351, I.353, P.355, V.358, T.377, M.379, L.383 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain C: E.278, R.439 Chain D: A.99, V.100 Ligands: EDO.27 Ligand excluded by PLIP EDO.21: 7 residues within 4Å: Chain C: G.182, G.183, A.184, K.198, I.202, F.217, D.218 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain C: P.253, N.279, R.439 Chain G: G.342, R.344, N.370 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain C: W.95, W.306, P.330, K.333 Chain F: L.340 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain D: W.95, R.105, N.106, N.111, V.301 Ligands: EDO.20 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain D: W.95, W.306, P.330, K.333 Chain G: L.340 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain C: A.99, V.100 Chain D: E.278, R.439 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain D: P.253, N.279, R.439 Chain F: G.342, R.344, N.370 Ligand excluded by PLIP EDO.31: 8 residues within 4Å: Chain D: P.350, G.351, I.353, P.355, V.358, T.377, M.379, L.383 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain E: E.278, R.439 Chain F: A.99, V.100 Ligands: EDO.43 Ligand excluded by PLIP EDO.37: 7 residues within 4Å: Chain E: G.182, G.183, A.184, K.198, I.202, F.217, D.218 Ligand excluded by PLIP EDO.38: 6 residues within 4Å: Chain C: G.342, R.344, N.370 Chain E: P.253, N.279, R.439 Ligand excluded by PLIP EDO.39: 5 residues within 4Å: Chain B: L.340 Chain E: W.95, W.306, P.330, K.333 Ligand excluded by PLIP EDO.43: 6 residues within 4Å: Chain F: W.95, R.105, N.106, N.111, V.301 Ligands: EDO.36 Ligand excluded by PLIP EDO.44: 5 residues within 4Å: Chain C: L.340 Chain F: W.95, W.306, P.330, K.333 Ligand excluded by PLIP EDO.45: 4 residues within 4Å: Chain E: A.99, V.100 Chain F: E.278, R.439 Ligand excluded by PLIP EDO.46: 6 residues within 4Å: Chain B: G.342, R.344, N.370 Chain F: P.253, N.279, R.439 Ligand excluded by PLIP EDO.47: 8 residues within 4Å: Chain F: P.350, G.351, I.353, P.355, V.358, T.377, M.379, L.383 Ligand excluded by PLIP EDO.52: 5 residues within 4Å: Chain G: E.278, R.439 Chain H: A.99, V.100 Ligands: EDO.59 Ligand excluded by PLIP EDO.53: 7 residues within 4Å: Chain G: G.182, G.183, A.184, K.198, I.202, F.217, D.218 Ligand excluded by PLIP EDO.54: 6 residues within 4Å: Chain A: G.342, R.344, N.370 Chain G: P.253, N.279, R.439 Ligand excluded by PLIP EDO.55: 5 residues within 4Å: Chain D: L.340 Chain G: W.95, W.306, P.330, K.333 Ligand excluded by PLIP EDO.59: 6 residues within 4Å: Chain H: W.95, R.105, N.106, N.111, V.301 Ligands: EDO.52 Ligand excluded by PLIP EDO.60: 5 residues within 4Å: Chain A: L.340 Chain H: W.95, W.306, P.330, K.333 Ligand excluded by PLIP EDO.61: 4 residues within 4Å: Chain G: A.99, V.100 Chain H: E.278, R.439 Ligand excluded by PLIP EDO.62: 6 residues within 4Å: Chain D: G.342, R.344, N.370 Chain H: P.253, N.279, R.439 Ligand excluded by PLIP EDO.63: 8 residues within 4Å: Chain H: P.350, G.351, I.353, P.355, V.358, T.377, M.379, L.383 Ligand excluded by PLIP

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

UNX.8: 7 residues within 4Å: Chain A: Q.288 Chain C: Q.288 Chain E: Q.288 Chain G: Q.288 Ligands: UNX.24, UNX.40, UNX.56 No protein-ligand interaction detected (PLIP) UNX.16: 7 residues within 4Å: Chain B: Q.288 Chain D: Q.288 Chain F: Q.288 Chain H: Q.288 Ligands: UNX.32, UNX.48, UNX.64 No protein-ligand interaction detected (PLIP) UNX.24: 7 residues within 4Å: Chain A: Q.288 Chain C: Q.288 Chain E: Q.288 Chain G: Q.288 Ligands: UNX.8, UNX.40, UNX.56 No protein-ligand interaction detected (PLIP) UNX.32: 7 residues within 4Å: Chain B: Q.288 Chain D: Q.288 Chain F: Q.288 Chain H: Q.288 Ligands: UNX.16, UNX.48, UNX.64 No protein-ligand interaction detected (PLIP) UNX.40: 7 residues within 4Å: Chain A: Q.288 Chain C: Q.288 Chain E: Q.288 Chain G: Q.288 Ligands: UNX.8, UNX.24, UNX.56 No protein-ligand interaction detected (PLIP) UNX.48: 7 residues within 4Å: Chain B: Q.288 Chain D: Q.288 Chain F: Q.288 Chain H: Q.288 Ligands: UNX.16, UNX.32, UNX.64 No protein-ligand interaction detected (PLIP) UNX.56: 7 residues within 4Å: Chain A: Q.288 Chain C: Q.288 Chain E: Q.288 Chain G: Q.288 Ligands: UNX.8, UNX.24, UNX.40 No protein-ligand interaction detected (PLIP) UNX.64: 7 residues within 4Å: Chain B: Q.288 Chain D: Q.288 Chain F: Q.288 Chain H: Q.288 Ligands: UNX.16, UNX.32, UNX.48 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Vetting, M.W. et al., Crystal structure of an enolase from pantoea ananatis (efi target efi-501676) with bound d-gluconate and mg. to be published

Release Date

2011-08-31

Peptides

Putative ManD family dehydratase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

Putative ManD family dehydratase