SMTL ID : 4d5g.1

Structure of recombinant CDH-H28AN484A

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

4 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Non-covalent)

FAD.1: 35 residues within 4Å: Chain A: H.153, G.213, G.214, G.215, R.218, S.219, T.239, S.240, T.241, A.257, G.258, F.259, C.260, G.261, G.279, S.280, R.281, L.282, S.283, W.285, G.286, D.302, T.303, D.304, V.307, A.320, D.321, A.322, I.398, T.402, F.406, S.420, M.421, A.422, G.424 33 PLIP interactions: 33 interactions with chain A Hydrophobic interactions: A:F.259, A:W.285, A:I.398, A:T.402 Hydrogen bonds: A:G.214, A:G.215, A:T.239, A:S.240, A:T.241, A:A.257, A:C.260, A:R.281, A:R.281, A:L.282, A:S.283, A:W.285, A:T.303, A:T.303, A:D.304, A:D.321, A:D.321, A:A.322, A:M.421 Water bridges: A:R.94, A:F.259, A:F.259, A:S.283, A:W.285, A:I.287, A:D.304, A:R.415 Salt bridges: A:R.281 pi-Stacking: A:F.406 FAD.14: 33 residues within 4Å: Chain B: H.153, G.213, G.214, G.215, R.218, S.219, T.239, S.240, T.241, A.257, G.258, F.259, C.260, G.261, G.279, S.280, R.281, L.282, S.283, W.285, G.286, D.302, T.303, D.304, V.307, A.320, D.321, A.322, F.406, S.420, M.421, A.422, G.424 30 PLIP interactions: 30 interactions with chain B Hydrophobic interactions: B:F.259, B:W.285 Hydrogen bonds: B:G.214, B:G.215, B:T.239, B:S.240, B:A.257, B:C.260, B:S.280, B:R.281, B:R.281, B:L.282, B:S.283, B:W.285, B:T.303, B:T.303, B:D.321, B:A.322, B:M.421 Water bridges: B:R.94, B:R.218, B:F.259, B:F.259, B:S.283, B:G.286, B:I.287, B:D.304, B:R.415 Salt bridges: B:R.281 pi-Stacking: B:F.406 FAD.23: 35 residues within 4Å: Chain C: H.153, G.213, G.214, G.215, R.218, S.219, T.239, S.240, T.241, A.257, G.258, F.259, C.260, G.261, G.279, S.280, R.281, L.282, S.283, W.285, G.286, D.302, T.303, D.304, V.307, A.320, D.321, A.322, I.398, T.402, F.406, S.420, M.421, A.422, G.424 32 PLIP interactions: 32 interactions with chain C Hydrophobic interactions: C:F.259, C:W.285, C:I.398, C:T.402 Hydrogen bonds: C:G.214, C:G.215, C:T.239, C:T.239, C:S.240, C:A.257, C:C.260, C:R.281, C:R.281, C:L.282, C:S.283, C:W.285, C:T.303, C:T.303, C:D.304, C:D.321, C:A.322, C:M.421 Water bridges: C:R.94, C:F.259, C:F.259, C:S.283, C:W.285, C:I.287, C:D.304, C:R.415 Salt bridges: C:R.281 pi-Stacking: C:F.406 FAD.36: 33 residues within 4Å: Chain D: H.153, G.213, G.214, G.215, R.218, S.219, T.239, S.240, T.241, A.257, G.258, F.259, C.260, G.261, G.279, S.280, R.281, L.282, S.283, W.285, G.286, D.302, T.303, D.304, V.307, A.320, D.321, A.322, F.406, S.420, M.421, A.422, G.424 33 PLIP interactions: 33 interactions with chain D Hydrophobic interactions: D:F.259, D:W.285 Hydrogen bonds: D:G.214, D:G.215, D:T.239, D:T.239, D:S.240, D:T.241, D:A.257, D:C.260, D:S.280, D:R.281, D:R.281, D:L.282, D:S.283, D:W.285, D:T.303, D:T.303, D:D.321, D:D.321, D:A.322, D:M.421 Water bridges: D:R.94, D:R.218, D:F.259, D:F.259, D:S.283, D:G.286, D:I.287, D:D.304, D:R.415 Salt bridges: D:R.281 pi-Stacking: D:F.406

4 x TPP: THIAMINE DIPHOSPHATE(Non-covalent)

TPP.2: 27 residues within 4Å: Chain A: I.398, G.399, N.400, H.401, G.424, I.425, L.426, G.450, D.451, G.452, A.453, Y.456, N.478, S.480, Y.481, G.482, A.483, N.484 Chain B: F.25, I.26, G.27, E.52, H.76, V.78, G.79, Q.116 Ligands: MG.3 21 PLIP interactions: 19 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.425, A:L.426, A:L.426, A:Y.481, A:Y.481, B:F.25 Hydrogen bonds: A:N.400, A:H.401, A:G.424, A:L.426, A:D.451, A:G.452, A:A.453, A:Y.456, A:N.478, A:S.480, A:G.482, A:A.483 Salt bridges: A:H.401, A:H.401 Water bridges: B:Q.116 TPP.15: 28 residues within 4Å: Chain A: F.25, I.26, G.27, E.52, H.76, V.78, G.79, L.82, Q.116 Chain B: I.398, G.399, N.400, H.401, G.424, I.425, L.426, G.450, D.451, G.452, A.453, Y.456, N.478, S.480, Y.481, G.482, A.483, N.484 Ligands: MG.16 17 PLIP interactions: 3 interactions with chain A, 14 interactions with chain B Hydrophobic interactions: A:F.25, A:L.82, B:I.425, B:L.426 Water bridges: A:G.79 Hydrogen bonds: B:N.400, B:H.401, B:G.424, B:L.426, B:D.451, B:G.452, B:A.453, B:S.480, B:G.482, B:A.483 Salt bridges: B:H.401, B:H.401 TPP.24: 27 residues within 4Å: Chain C: I.398, G.399, N.400, H.401, G.424, I.425, L.426, G.450, D.451, G.452, A.453, Y.456, N.478, S.480, Y.481, G.482, A.483, N.484 Chain D: F.25, I.26, G.27, E.52, H.76, V.78, G.79, Q.116 Ligands: MG.25 20 PLIP interactions: 18 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:I.425, C:L.426, C:L.426, C:Y.481, C:Y.481, D:F.25 Hydrogen bonds: C:N.400, C:H.401, C:G.424, C:L.426, C:D.451, C:G.452, C:A.453, C:N.478, C:S.480, C:G.482, C:A.483 Salt bridges: C:H.401, C:H.401 Water bridges: D:Q.116 TPP.37: 28 residues within 4Å: Chain C: F.25, I.26, G.27, E.52, H.76, V.78, G.79, L.82, Q.116 Chain D: I.398, G.399, N.400, H.401, G.424, I.425, L.426, G.450, D.451, G.452, A.453, Y.456, N.478, S.480, Y.481, G.482, A.483, N.484 Ligands: MG.38 19 PLIP interactions: 16 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:I.425, D:L.426, C:F.25, C:L.82 Hydrogen bonds: D:N.400, D:H.401, D:G.424, D:L.426, D:D.451, D:G.452, D:A.453, D:Y.456, D:N.478, D:S.480, D:G.482, D:A.483 Salt bridges: D:H.401, D:H.401 Water bridges: C:E.52

6 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.3: 4 residues within 4Å: Chain A: D.451, N.478, S.480 Ligands: TPP.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.451, A:S.480, H2O.11 MG.13: 1 residues within 4Å: Ligands: PG4.11 No protein-ligand interaction detected (PLIP) MG.16: 5 residues within 4Å: Chain B: D.451, N.478, S.480, G.482 Ligands: TPP.15 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.451, B:S.480, H2O.21 MG.25: 4 residues within 4Å: Chain C: D.451, N.478, S.480 Ligands: TPP.24 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.451, C:S.480, H2O.34 MG.35: 1 residues within 4Å: Ligands: PG4.33 No protein-ligand interaction detected (PLIP) MG.38: 5 residues within 4Å: Chain D: D.451, N.478, S.480, G.482 Ligands: TPP.37 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.451, D:S.480, H2O.44

18 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 5 residues within 4Å: Chain A: P.441, S.443, R.444, P.470 Ligands: PG4.7 Ligand excluded by PLIP PG4.6: 5 residues within 4Å: Chain A: E.368, R.379, A.382, R.385, K.386 Ligand excluded by PLIP PG4.7: 4 residues within 4Å: Chain A: I.533, D.534, G.536 Ligands: PG4.4 Ligand excluded by PLIP PG4.8: 6 residues within 4Å: Chain A: E.134, R.135 Chain B: R.568 Chain C: R.568 Chain D: E.134, R.135 Ligand excluded by PLIP PG4.11: 4 residues within 4Å: Chain A: E.15, E.16, H.41 Ligands: MG.13 Ligand excluded by PLIP PG4.12: 7 residues within 4Å: Chain A: A.109, Q.117, V.118, P.119, W.120, R.132 Chain D: E.134 Ligand excluded by PLIP PG4.19: 9 residues within 4Å: Chain B: F.147, R.148, E.151, R.183, A.184 Chain D: P.305, L.308 Ligands: 2PE.18, 2PE.40 Ligand excluded by PLIP PG4.20: 5 residues within 4Å: Chain B: R.91, T.124, A.127, R.128 Ligands: PG4.42 Ligand excluded by PLIP PG4.22: 8 residues within 4Å: Chain B: A.109, Q.117, V.118, P.119, W.120, R.132 Chain C: R.132, E.134 Ligand excluded by PLIP PG4.26: 5 residues within 4Å: Chain C: P.441, S.443, R.444, P.470 Ligands: PG4.29 Ligand excluded by PLIP PG4.28: 5 residues within 4Å: Chain C: E.368, R.379, A.382, R.385, K.386 Ligand excluded by PLIP PG4.29: 4 residues within 4Å: Chain C: I.533, D.534, G.536 Ligands: PG4.26 Ligand excluded by PLIP PG4.30: 6 residues within 4Å: Chain A: R.568 Chain B: E.134, R.135 Chain C: E.134, R.135 Chain D: R.568 Ligand excluded by PLIP PG4.33: 4 residues within 4Å: Chain C: E.15, E.16, H.41 Ligands: MG.35 Ligand excluded by PLIP PG4.34: 7 residues within 4Å: Chain B: E.134 Chain C: A.109, Q.117, V.118, P.119, W.120, R.132 Ligand excluded by PLIP PG4.41: 9 residues within 4Å: Chain B: P.305, L.308 Chain D: F.147, R.148, E.151, R.183, A.184 Ligands: 2PE.18, 2PE.40 Ligand excluded by PLIP PG4.42: 5 residues within 4Å: Chain D: R.91, T.124, A.127, R.128 Ligands: PG4.20 Ligand excluded by PLIP PG4.44: 8 residues within 4Å: Chain A: R.132, E.134 Chain D: A.109, Q.117, V.118, P.119, W.120, R.132 Ligand excluded by PLIP

2 x 1PG: 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL(Non-covalent)

1PG.5: 3 residues within 4Å: Chain A: G.513, A.514, K.537 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.537 1PG.27: 3 residues within 4Å: Chain C: G.513, A.514, K.537 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.537

6 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.9: 5 residues within 4Å: Chain A: R.91, T.124, P.125, A.127, R.128 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.91, A:R.91 PEG.10: 1 residues within 4Å: Chain A: Q.494 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.494 PEG.21: 5 residues within 4Å: Chain B: E.366, S.369, P.374, S.376, Q.549 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.369, B:P.374 PEG.31: 5 residues within 4Å: Chain C: R.91, T.124, P.125, A.127, R.128 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.91, C:R.91 PEG.32: 1 residues within 4Å: Chain C: Q.494 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.494 PEG.43: 5 residues within 4Å: Chain D: E.366, S.369, P.374, S.376, Q.549 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.369, D:P.374

4 x 2PE: NONAETHYLENE GLYCOL(Non-covalent)

2PE.17: 9 residues within 4Å: Chain B: V.387, Q.388, R.389, P.390, P.441, N.442, S.443, R.444, P.470 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.444, B:R.444 2PE.18: 21 residues within 4Å: Chain B: E.151, H.153, A.184, K.185, S.186, L.188, T.303, P.305, V.319 Chain D: E.151, H.153, R.183, A.184, K.185, S.186, L.188, T.303, P.305 Ligands: PG4.19, 2PE.40, PG4.41 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:E.151, B:H.153, D:E.151 Water bridges: D:S.186 2PE.39: 9 residues within 4Å: Chain D: V.387, Q.388, R.389, P.390, P.441, N.442, S.443, R.444, P.470 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.444, D:R.444 2PE.40: 21 residues within 4Å: Chain B: E.151, H.153, R.183, A.184, K.185, S.186, L.188, T.303, P.305 Chain D: E.151, H.153, A.184, K.185, S.186, L.188, T.303, P.305, V.319 Ligands: 2PE.18, PG4.19, PG4.41 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:E.151, B:H.153, D:E.151 Water bridges: B:S.186

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Loschonsky, S. et al., Extended Reaction Scope of Thiamine Diphosphate Dependent Cyclohexane-1,2-Dione Hydrolase: From C-C Bond Cleavage to C-C Bond Ligation. Angew.Chem.Int.Ed.Engl. (2014)

Release Date

2015-01-21

Peptides

CYCLOHEXANE-1,2-DIONE HYDROLASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

CYCLOHEXANE-1,2-DIONE HYDROLASE