SMTL ID : 4c22.1

L-Fucose Isomerase In Complex With Fuculose

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-hexamer

Ligands

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

MN.1: 5 residues within 4Å: Chain A: E.351, D.375, N.540, H.541 Ligands: CVU.3 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.351, A:D.375, A:D.375, A:H.541, H2O.6 MN.11: 5 residues within 4Å: Chain B: E.351, D.375, N.540, H.541 Ligands: CVU.13 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.351, B:D.375, B:D.375, B:H.541, H2O.14 MN.21: 5 residues within 4Å: Chain C: E.351, D.375, N.540, H.541 Ligands: CVU.23 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.351, C:D.375, C:D.375, C:H.541, H2O.23 MN.31: 5 residues within 4Å: Chain D: E.351, D.375, N.540, H.541 Ligands: CVU.33 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:E.351, D:D.375, D:D.375, D:H.541, H2O.32 MN.41: 5 residues within 4Å: Chain E: E.351, D.375, N.540, H.541 Ligands: CVU.43 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.351, E:D.375, E:D.375, E:H.541, H2O.41 MN.51: 5 residues within 4Å: Chain F: E.351, D.375, N.540, H.541 Ligands: CVU.53 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:E.351, F:D.375, F:D.375, F:H.541, H2O.49

6 x FUC: alpha-L-fucopyranose(Non-covalent)

FUC.2: 8 residues within 4Å: Chain A: W.247, N.251, D.338, G.341, E.434, V.437, Q.438, L.441 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.441 Hydrogen bonds: A:D.338, A:G.341, A:E.434 FUC.12: 10 residues within 4Å: Chain B: W.247, N.251, F.337, D.338, G.341, I.342, E.434, V.437, Q.438, L.441 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.247, B:L.441 Hydrogen bonds: B:D.338, B:E.434, B:E.434 FUC.22: 8 residues within 4Å: Chain C: W.247, N.251, D.338, G.341, E.434, V.437, Q.438, L.441 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.441 Hydrogen bonds: C:D.338, C:G.341, C:E.434 FUC.32: 10 residues within 4Å: Chain D: W.247, N.251, F.337, D.338, G.341, I.342, E.434, V.437, Q.438, L.441 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:W.247, D:L.441 Hydrogen bonds: D:D.338, D:E.434, D:E.434 FUC.42: 8 residues within 4Å: Chain E: W.247, N.251, D.338, G.341, E.434, V.437, Q.438, L.441 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:L.441 Hydrogen bonds: E:D.338, E:G.341, E:E.434 FUC.52: 10 residues within 4Å: Chain F: W.247, N.251, F.337, D.338, G.341, I.342, E.434, V.437, Q.438, L.441 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:W.247, F:L.441 Hydrogen bonds: F:D.338, F:E.434, F:E.434

6 x CVU: L-Fuculose open form(Non-covalent)

CVU.3: 14 residues within 4Å: Chain A: M.199, Q.316, E.351, D.375, S.407, Y.453, W.512, N.540, H.541 Chain C: R.32, W.104, P.130, V.133 Ligands: MN.1 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:Y.453, A:W.512 Hydrogen bonds: A:Q.316, A:S.407, A:N.540, C:R.32, C:R.32 Water bridges: A:S.407 CVU.13: 15 residues within 4Å: Chain B: M.199, I.201, Q.316, E.351, D.375, S.407, Y.453, W.512, N.540, H.541 Chain F: R.32, W.104, P.130, V.133 Ligands: MN.11 10 PLIP interactions: 7 interactions with chain B, 3 interactions with chain F Hydrophobic interactions: B:Y.453, B:W.512 Hydrogen bonds: B:Q.316, B:E.351, B:S.407, B:N.540, F:R.32, F:R.32, F:W.104 Water bridges: B:S.407 CVU.23: 14 residues within 4Å: Chain C: M.199, Q.316, E.351, D.375, S.407, Y.453, W.512, N.540, H.541 Chain E: R.32, W.104, P.130, V.133 Ligands: MN.21 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain E Hydrophobic interactions: C:Y.453, C:W.512 Hydrogen bonds: C:Q.316, C:S.407, C:N.540, E:R.32, E:R.32 Water bridges: C:S.407 CVU.33: 15 residues within 4Å: Chain B: R.32, W.104, P.130, V.133 Chain D: M.199, I.201, Q.316, E.351, D.375, S.407, Y.453, W.512, N.540, H.541 Ligands: MN.31 10 PLIP interactions: 7 interactions with chain D, 3 interactions with chain B Hydrophobic interactions: D:Y.453, D:W.512 Hydrogen bonds: D:Q.316, D:E.351, D:S.407, D:N.540, B:R.32, B:R.32, B:W.104 Water bridges: D:S.407 CVU.43: 14 residues within 4Å: Chain A: R.32, W.104, P.130, V.133 Chain E: M.199, Q.316, E.351, D.375, S.407, Y.453, W.512, N.540, H.541 Ligands: MN.41 8 PLIP interactions: 6 interactions with chain E, 2 interactions with chain A Hydrophobic interactions: E:Y.453, E:W.512 Hydrogen bonds: E:Q.316, E:S.407, E:N.540, A:R.32, A:R.32 Water bridges: E:S.407 CVU.53: 15 residues within 4Å: Chain D: R.32, W.104, P.130, V.133 Chain F: M.199, I.201, Q.316, E.351, D.375, S.407, Y.453, W.512, N.540, H.541 Ligands: MN.51 10 PLIP interactions: 7 interactions with chain F, 3 interactions with chain D Hydrophobic interactions: F:Y.453, F:W.512 Hydrogen bonds: F:Q.316, F:E.351, F:S.407, F:N.540, D:R.32, D:R.32, D:W.104 Water bridges: F:S.407

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

EDO.4: 11 residues within 4Å: Chain A: E.330, N.334, F.348, T.350, Q.371, I.372, F.373, N.406, S.409, C.410, T.411 Ligand excluded by PLIP EDO.5: 8 residues within 4Å: Chain A: G.31, R.33, R.37, R.78, E.81 Chain F: L.8, E.301, V.304 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: D.116, I.117, T.183, R.187, L.215, L.602, H.603 Ligand excluded by PLIP EDO.7: 5 residues within 4Å: Chain A: P.115 Chain F: R.187, D.188, G.216, H.603 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: R.187, D.188, G.216, H.603 Chain F: P.115 Ligand excluded by PLIP EDO.9: 9 residues within 4Å: Chain A: R.26, T.97, I.98, T.99, M.111, D.112, A.120, I.121, H.142 Ligand excluded by PLIP EDO.10: 7 residues within 4Å: Chain A: L.135, A.136, L.139, K.578 Chain E: M.534, N.535, W.537 Ligand excluded by PLIP EDO.14: 9 residues within 4Å: Chain B: I.554, A.557, S.558, I.562, P.563, V.564, R.576, D.592, C.596 Ligand excluded by PLIP EDO.15: 11 residues within 4Å: Chain B: R.26, T.97, T.99, M.111, D.112, H.119, A.120, I.121, Y.134, V.138, H.142 Ligand excluded by PLIP EDO.16: 9 residues within 4Å: Chain B: T.183, M.186, R.187, Y.214, L.215, G.216, L.560, L.602, H.603 Ligand excluded by PLIP EDO.17: 11 residues within 4Å: Chain B: E.330, N.334, F.348, T.350, Q.371, I.372, F.373, N.406, S.409, C.410, T.411 Ligand excluded by PLIP EDO.18: 8 residues within 4Å: Chain B: M.534, N.535, W.537 Chain F: L.135, A.136, L.139, G.151, K.578 Ligand excluded by PLIP EDO.19: 7 residues within 4Å: Chain B: E.226, R.230, E.301, E.302, G.305, H.306 Chain C: R.78 Ligand excluded by PLIP EDO.20: 11 residues within 4Å: Chain B: F.124, N.125, G.126, R.129, P.130, G.131, A.132, Y.153 Chain D: R.377, T.378, Y.379 Ligand excluded by PLIP EDO.24: 11 residues within 4Å: Chain C: E.330, N.334, F.348, T.350, Q.371, I.372, F.373, N.406, S.409, C.410, T.411 Ligand excluded by PLIP EDO.25: 8 residues within 4Å: Chain B: L.8, E.301, V.304 Chain C: G.31, R.33, R.37, R.78, E.81 Ligand excluded by PLIP EDO.26: 7 residues within 4Å: Chain C: D.116, I.117, T.183, R.187, L.215, L.602, H.603 Ligand excluded by PLIP EDO.27: 5 residues within 4Å: Chain B: R.187, D.188, G.216, H.603 Chain C: P.115 Ligand excluded by PLIP EDO.28: 5 residues within 4Å: Chain B: P.115 Chain C: R.187, D.188, G.216, H.603 Ligand excluded by PLIP EDO.29: 9 residues within 4Å: Chain C: R.26, T.97, I.98, T.99, M.111, D.112, A.120, I.121, H.142 Ligand excluded by PLIP EDO.30: 7 residues within 4Å: Chain A: M.534, N.535, W.537 Chain C: L.135, A.136, L.139, K.578 Ligand excluded by PLIP EDO.34: 9 residues within 4Å: Chain D: I.554, A.557, S.558, I.562, P.563, V.564, R.576, D.592, C.596 Ligand excluded by PLIP EDO.35: 11 residues within 4Å: Chain D: R.26, T.97, T.99, M.111, D.112, H.119, A.120, I.121, Y.134, V.138, H.142 Ligand excluded by PLIP EDO.36: 9 residues within 4Å: Chain D: T.183, M.186, R.187, Y.214, L.215, G.216, L.560, L.602, H.603 Ligand excluded by PLIP EDO.37: 11 residues within 4Å: Chain D: E.330, N.334, F.348, T.350, Q.371, I.372, F.373, N.406, S.409, C.410, T.411 Ligand excluded by PLIP EDO.38: 8 residues within 4Å: Chain B: L.135, A.136, L.139, G.151, K.578 Chain D: M.534, N.535, W.537 Ligand excluded by PLIP EDO.39: 7 residues within 4Å: Chain D: E.226, R.230, E.301, E.302, G.305, H.306 Chain E: R.78 Ligand excluded by PLIP EDO.40: 11 residues within 4Å: Chain D: F.124, N.125, G.126, R.129, P.130, G.131, A.132, Y.153 Chain F: R.377, T.378, Y.379 Ligand excluded by PLIP EDO.44: 11 residues within 4Å: Chain E: E.330, N.334, F.348, T.350, Q.371, I.372, F.373, N.406, S.409, C.410, T.411 Ligand excluded by PLIP EDO.45: 8 residues within 4Å: Chain D: L.8, E.301, V.304 Chain E: G.31, R.33, R.37, R.78, E.81 Ligand excluded by PLIP EDO.46: 7 residues within 4Å: Chain E: D.116, I.117, T.183, R.187, L.215, L.602, H.603 Ligand excluded by PLIP EDO.47: 5 residues within 4Å: Chain D: R.187, D.188, G.216, H.603 Chain E: P.115 Ligand excluded by PLIP EDO.48: 5 residues within 4Å: Chain D: P.115 Chain E: R.187, D.188, G.216, H.603 Ligand excluded by PLIP EDO.49: 9 residues within 4Å: Chain E: R.26, T.97, I.98, T.99, M.111, D.112, A.120, I.121, H.142 Ligand excluded by PLIP EDO.50: 7 residues within 4Å: Chain C: M.534, N.535, W.537 Chain E: L.135, A.136, L.139, K.578 Ligand excluded by PLIP EDO.54: 9 residues within 4Å: Chain F: I.554, A.557, S.558, I.562, P.563, V.564, R.576, D.592, C.596 Ligand excluded by PLIP EDO.55: 11 residues within 4Å: Chain F: R.26, T.97, T.99, M.111, D.112, H.119, A.120, I.121, Y.134, V.138, H.142 Ligand excluded by PLIP EDO.56: 9 residues within 4Å: Chain F: T.183, M.186, R.187, Y.214, L.215, G.216, L.560, L.602, H.603 Ligand excluded by PLIP EDO.57: 11 residues within 4Å: Chain F: E.330, N.334, F.348, T.350, Q.371, I.372, F.373, N.406, S.409, C.410, T.411 Ligand excluded by PLIP EDO.58: 8 residues within 4Å: Chain D: L.135, A.136, L.139, G.151, K.578 Chain F: M.534, N.535, W.537 Ligand excluded by PLIP EDO.59: 7 residues within 4Å: Chain A: R.78 Chain F: E.226, R.230, E.301, E.302, G.305, H.306 Ligand excluded by PLIP EDO.60: 11 residues within 4Å: Chain B: R.377, T.378, Y.379 Chain F: F.124, N.125, G.126, R.129, P.130, G.131, A.132, Y.153 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Higgins, M.A. et al., Structural and Functional Analysis of Fucose-Processing Enzymes from Streptococcus Pneumoniae. J.Mol.Biol. (2014)

Release Date

2013-12-11

Peptides

L-FUCOSE ISOMERASE: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

L-FUCOSE ISOMERASE