SMTL ID : 3ktc.1

Crystal structure of Putative sugar isomerase (YP_050048.1) from ERWINIA CAROTOVORA ATROSEPTICA SCRI1043 at 1.54 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

homo-tetramer

Ligands

8 x FE: FE (III) ION(Non-covalent)

FE.1: 5 residues within 4Å: Chain A: D.202, H.205, D.239, D.241 Ligands: UNL.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.205, A:D.239, A:D.239, A:D.241, H2O.14 FE.2: 6 residues within 4Å: Chain A: E.167, D.202, H.205, D.230, D.271 Ligands: UNL.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.167, A:D.202, A:D.230, A:D.271 FE.13: 7 residues within 4Å: Chain B: K.169, D.202, H.205, D.239, D.241, D.271 Ligands: UNL.17 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.205, B:D.239, H2O.28 FE.14: 6 residues within 4Å: Chain B: E.167, D.202, H.205, D.230, D.271 Ligands: UNL.17 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.167, B:D.202, B:D.230, B:D.271 FE.27: 5 residues within 4Å: Chain C: D.202, H.205, D.239, D.241 Ligands: UNL.31 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:H.205, C:D.239, C:D.239, C:D.241, H2O.41 FE.28: 6 residues within 4Å: Chain C: E.167, D.202, H.205, D.230, D.271 Ligands: UNL.31 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:E.167, C:D.202, C:D.230, C:D.271 FE.39: 7 residues within 4Å: Chain D: K.169, D.202, H.205, D.239, D.241, D.271 Ligands: UNL.43 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:H.205, D:D.239, H2O.55 FE.40: 6 residues within 4Å: Chain D: E.167, D.202, H.205, D.230, D.271 Ligands: UNL.43 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:E.167, D:D.202, D:D.230, D:D.271

4 x MG: MAGNESIUM ION(Non-functional Binders)

MG.3: 1 residues within 4Å: Ligands: UNL.6 No protein-ligand interaction detected (PLIP) MG.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.29: 1 residues within 4Å: Ligands: UNL.32 No protein-ligand interaction detected (PLIP) MG.41: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

CL.4: 5 residues within 4Å: Chain A: I.221, G.224, R.225, L.226, W.264 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain B: I.221, G.224, R.225, L.226 Ligand excluded by PLIP CL.30: 5 residues within 4Å: Chain C: I.221, G.224, R.225, L.226, W.264 Ligand excluded by PLIP CL.42: 4 residues within 4Å: Chain D: I.221, G.224, R.225, L.226 Ligand excluded by PLIP

6 x UNL: UNKNOWN LIGAND

UNL.5: 16 residues within 4Å: Chain A: W.15, T.81, Y.85, K.125, W.127, E.167, K.169, D.202, H.205, D.230, D.239, D.271, F.273 Chain C: Y.24 Ligands: FE.1, FE.2 8 PLIP interactions: 7 interactions with chain A, 1 interactions with chain C Hydrogen bonds: A:Y.85, A:K.125, A:K.125, A:W.127, A:E.167, A:K.169, A:D.271, C:Y.24 UNL.6: 5 residues within 4Å: Chain A: K.260, I.302, P.303, Q.306 Ligands: MG.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.260, A:K.260, A:Q.306 Water bridges: A:L.300 UNL.17: 16 residues within 4Å: Chain B: W.15, T.81, Y.85, K.125, W.127, E.167, K.169, D.202, H.205, D.230, D.239, D.271, F.273 Chain D: Y.24 Ligands: FE.13, FE.14 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:Y.85, B:K.125, B:K.125, B:K.125, B:W.127, B:E.167, D:Y.24 Water bridges: B:Y.85 UNL.31: 16 residues within 4Å: Chain A: Y.24 Chain C: W.15, T.81, Y.85, K.125, W.127, E.167, K.169, D.202, H.205, D.230, D.239, D.271, F.273 Ligands: FE.27, FE.28 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:Y.85, C:Y.85, C:K.125, C:K.125, C:E.167, C:D.202, C:D.230, C:D.271, A:Y.24 Water bridges: C:D.239, A:Y.24 UNL.32: 5 residues within 4Å: Chain C: K.260, I.302, P.303, Q.306 Ligands: MG.29 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.260, C:K.260, C:Q.306 Water bridges: C:L.300 UNL.43: 16 residues within 4Å: Chain B: Y.24 Chain D: W.15, T.81, Y.85, K.125, W.127, E.167, K.169, D.202, H.205, D.230, D.239, D.271, F.273 Ligands: FE.39, FE.40 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:Y.85, D:Y.85, D:K.125, D:K.125, D:E.167, D:K.169

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

EDO.7: 7 residues within 4Å: Chain A: W.133, K.176, M.177, T.178, D.180, R.184 Chain B: D.215 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: P.160, D.161, K.163, N.196 Ligand excluded by PLIP EDO.9: 8 residues within 4Å: Chain A: I.78, N.122, Y.123, F.227, G.228, W.264, G.266, V.267 Ligand excluded by PLIP EDO.10: 9 residues within 4Å: Chain A: G.210, E.211, S.212, D.215, S.216 Chain B: K.176, D.180, R.184 Ligands: EDO.21 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: Y.29, F.275, R.276 Chain C: S.90, R.91 Ligand excluded by PLIP EDO.12: 4 residues within 4Å: Chain A: Q.218, I.261, N.262 Chain B: K.142 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain B: E.190, R.223, R.225 Ligand excluded by PLIP EDO.19: 4 residues within 4Å: Chain A: K.142 Chain B: Q.218, I.261, N.262 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain B: P.160, D.161, K.163, N.196 Ligand excluded by PLIP EDO.21: 8 residues within 4Å: Chain A: D.215 Chain B: W.133, K.176, M.177, T.178, D.180, R.184 Ligands: EDO.10 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain B: Y.29, F.275, R.276 Chain D: S.90, R.91 Ligand excluded by PLIP EDO.23: 8 residues within 4Å: Chain B: I.78, N.122, Y.123, F.227, G.228, Q.265, G.266, V.267 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain A: Q.309, E.310, Q.312 Chain B: V.139, S.140, N.143, L.144 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain B: E.47, L.48, S.49 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain B: L.14, T.35, L.53, P.54, F.57 Ligand excluded by PLIP EDO.33: 7 residues within 4Å: Chain C: W.133, K.176, M.177, T.178, D.180, R.184 Chain D: D.215 Ligand excluded by PLIP EDO.34: 4 residues within 4Å: Chain C: P.160, D.161, K.163, N.196 Ligand excluded by PLIP EDO.35: 8 residues within 4Å: Chain C: I.78, N.122, Y.123, F.227, G.228, W.264, G.266, V.267 Ligand excluded by PLIP EDO.36: 9 residues within 4Å: Chain C: G.210, E.211, S.212, D.215, S.216 Chain D: K.176, D.180, R.184 Ligands: EDO.47 Ligand excluded by PLIP EDO.37: 5 residues within 4Å: Chain A: S.90, R.91 Chain C: Y.29, F.275, R.276 Ligand excluded by PLIP EDO.38: 4 residues within 4Å: Chain C: Q.218, I.261, N.262 Chain D: K.142 Ligand excluded by PLIP EDO.44: 3 residues within 4Å: Chain D: E.190, R.223, R.225 Ligand excluded by PLIP EDO.45: 4 residues within 4Å: Chain C: K.142 Chain D: Q.218, I.261, N.262 Ligand excluded by PLIP EDO.46: 4 residues within 4Å: Chain D: P.160, D.161, K.163, N.196 Ligand excluded by PLIP EDO.47: 8 residues within 4Å: Chain C: D.215 Chain D: W.133, K.176, M.177, T.178, D.180, R.184 Ligands: EDO.36 Ligand excluded by PLIP EDO.48: 5 residues within 4Å: Chain B: S.90, R.91 Chain D: Y.29, F.275, R.276 Ligand excluded by PLIP EDO.49: 8 residues within 4Å: Chain D: I.78, N.122, Y.123, F.227, G.228, Q.265, G.266, V.267 Ligand excluded by PLIP EDO.50: 7 residues within 4Å: Chain C: Q.309, E.310, Q.312 Chain D: V.139, S.140, N.143, L.144 Ligand excluded by PLIP EDO.51: 3 residues within 4Å: Chain D: E.47, L.48, S.49 Ligand excluded by PLIP EDO.52: 5 residues within 4Å: Chain D: L.14, T.35, L.53, P.54, F.57 Ligand excluded by PLIP

Links

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Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of Putative sugar isomerase (YP_050048.1) from ERWINIA CAROTOVORA ATROSEPTICA SCRI1043 at 1.54 A resolution. To be published

Release Date

2009-12-22

Peptides

Xylose isomerase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Xylose isomerase