SMTL ID : 6wn6.2 (1 other biounit)

Crystal structure of 3-keto-D-glucoside 4-epimerase, YcjR, from E. coli, apo form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: E.198, D.231, H.257, E.292 Ligands: EDO.3 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.198, A:D.231, A:H.257, A:E.292 MN.20: 5 residues within 4Å: Chain B: E.198, D.231, H.257, E.292 Ligands: EDO.21 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.198, B:D.231, B:H.257, B:E.292

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

EDO.2: 5 residues within 4Å: Chain A: G.293, R.294 Ligands: EDO.3, EDO.5, EDO.7 Ligand excluded by PLIP EDO.3: 10 residues within 4Å: Chain A: W.154, E.198, L.200, Q.204, H.234, R.263, E.292 Ligands: MN.1, EDO.2, EDO.7 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: Q.58, N.59, F.82, E.83, I.84, D.85 Ligands: EDO.5 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: Q.58, N.59, Q.60, E.292, G.293 Ligands: EDO.2, EDO.4 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: G.112, G.113, Y.114, W.117 Ligands: EDO.8 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: W.154 Chain B: R.160, M.164 Ligands: EDO.2, EDO.3 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: C.111, G.112, P.151 Ligands: EDO.6 Ligand excluded by PLIP EDO.9: 13 residues within 4Å: Chain A: Q.60, I.258, A.259, R.263, Y.264, Q.265, P.266, Y.291, E.292, G.293, R.294, I.295, Y.304 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: H.206, M.207, N.209, D.213 Ligands: EDO.11 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: T.210, A.212, D.213 Chain B: R.296 Ligands: EDO.10 Ligand excluded by PLIP EDO.12: 6 residues within 4Å: Chain A: L.170, D.173, R.174, M.207, Y.217 Ligands: EDO.13 Ligand excluded by PLIP EDO.13: 6 residues within 4Å: Chain A: R.174, D.213, R.216, Y.217 Ligands: EDO.12, EDO.14 Ligand excluded by PLIP EDO.14: 6 residues within 4Å: Chain A: R.174, S.178, R.216, Y.217, E.220 Ligands: EDO.13 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: L.242, L.271, D.272 Chain B: T.270 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: H.262, Y.264, S.268, R.296 Chain B: D.240 Ligand excluded by PLIP EDO.17: 1 residues within 4Å: Chain A: R.190 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: N.59, E.65, K.70, L.88 Ligand excluded by PLIP EDO.19: 6 residues within 4Å: Chain A: K.52, M.53, K.54, Y.285, Q.286, G.287 Ligand excluded by PLIP EDO.21: 10 residues within 4Å: Chain B: E.198, L.200, Q.204, H.234, R.263, E.292 Ligands: MN.20, EDO.22, EDO.23, EDO.26 Ligand excluded by PLIP EDO.22: 4 residues within 4Å: Chain A: R.160 Chain B: W.154 Ligands: EDO.21, EDO.23 Ligand excluded by PLIP EDO.23: 8 residues within 4Å: Chain A: R.160 Chain B: R.263, E.292, G.293, R.294 Ligands: EDO.21, EDO.22, EDO.24 Ligand excluded by PLIP EDO.24: 7 residues within 4Å: Chain B: Q.58, N.59, Q.60, E.292, G.293 Ligands: EDO.23, EDO.30 Ligand excluded by PLIP EDO.25: 13 residues within 4Å: Chain B: Q.60, I.258, A.259, R.263, Y.264, Q.265, P.266, Y.291, E.292, G.293, R.294, I.295, Y.304 Ligand excluded by PLIP EDO.26: 6 residues within 4Å: Chain B: C.111, G.112, W.117, P.151 Ligands: EDO.21, EDO.32 Ligand excluded by PLIP EDO.27: 6 residues within 4Å: Chain B: L.170, D.173, R.174, M.207, Y.217 Ligands: EDO.35 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain B: H.206, M.207, N.209, D.213 Ligands: EDO.29 Ligand excluded by PLIP EDO.29: 5 residues within 4Å: Chain A: R.296 Chain B: T.210, D.213, R.216 Ligands: EDO.28 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain B: Q.58, N.59, E.83, I.84, D.85 Ligands: EDO.24 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain A: R.160, R.202 Chain B: Y.264, R.294 Ligand excluded by PLIP EDO.32: 6 residues within 4Å: Chain B: D.85, G.112, G.113, Y.114, W.117 Ligands: EDO.26 Ligand excluded by PLIP EDO.33: 4 residues within 4Å: Chain A: T.270 Chain B: L.242, L.271, D.272 Ligand excluded by PLIP EDO.34: 7 residues within 4Å: Chain B: R.174, S.178, R.216, Y.217, E.220, N.221 Ligands: EDO.35 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain B: R.174, D.213, R.216, Y.217 Ligands: EDO.27, EDO.34 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain A: D.240, N.241 Chain B: G.267, S.268, G.269 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mabanglo, M.F. et al., Structure and Reaction Mechanism of YcjR, an Epimerase That Facilitates the Interconversion of d-Gulosides to d-Glucosides inEscherichia coli. Biochemistry (2020)

Release Date

2020-06-10

Peptides

3-keto-D-glucoside 4-epimerase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

3-keto-D-glucoside 4-epimerase

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