SMTL ID : 5i2h.1

Crystal structure of O-methyltransferase family 2 protein Plim_1147 from Planctomyces limnophilus DSM 3776 complex with Apigenin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

homo-dimer

Ligands

2 x AGI: 5,7-dihydroxy-2-(4-hydroxyphenyl)-4H-chromen-4-one(Non-covalent)

AGI.1: 9 residues within 4Å: Chain A: L.161, L.165, R.168, N.270, H.273, D.274, Y.317, L.324 Chain B: Y.109 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:L.161, A:L.161, A:L.165, A:L.324 Hydrogen bonds: A:R.168, A:R.168, A:D.274, B:Y.109, B:Y.109 AGI.9: 9 residues within 4Å: Chain A: Y.109 Chain B: L.161, L.165, R.168, N.270, H.273, D.274, Y.317, L.324 11 PLIP interactions: 1 interactions with chain A, 10 interactions with chain B Hydrogen bonds: A:Y.109, B:R.168, B:R.168, B:D.274, B:Y.317 Hydrophobic interactions: B:L.161, B:L.161, B:L.165, B:L.165, B:L.324, B:L.324

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

EDO.2: 4 residues within 4Å: Chain A: S.116, A.117 Chain B: A.117, G.118 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Water bridges: B:G.118, A:S.116, A:S.116 Hydrogen bonds: A:A.117 EDO.3: 1 residues within 4Å: Chain A: D.153 No protein-ligand interaction detected (PLIP) EDO.4: 4 residues within 4Å: Chain A: D.227, G.253, D.254, M.255 1 PLIP interactions: 1 interactions with chain A Water bridges: A:W.256 EDO.5: 3 residues within 4Å: Chain A: A.117 Chain B: A.117 Ligands: EDO.15 No protein-ligand interaction detected (PLIP) EDO.10: 4 residues within 4Å: Chain B: A.281, R.282, A.285 Ligands: EDO.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.282 Water bridges: B:P.278, B:R.282 EDO.11: 9 residues within 4Å: Chain B: R.168, Y.210, N.270, V.302, Y.317, S.353, A.354, G.356 Ligands: FMT.19 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.210, B:Y.210, B:N.270, B:Y.317 Water bridges: B:R.168 EDO.12: 7 residues within 4Å: Chain B: A.281, A.285, G.337, W.338, G.341, A.342 Ligands: EDO.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.337 Water bridges: B:G.341 EDO.13: 4 residues within 4Å: Chain B: N.305, T.309, G.310, P.311 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.309 Water bridges: B:L.312 EDO.14: 5 residues within 4Å: Chain A: A.29 Chain B: D.22, L.23, G.26, L.316 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:L.23 EDO.15: 6 residues within 4Å: Chain A: A.117, G.118 Chain B: S.116, A.117, G.118 Ligands: EDO.5 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.116, B:A.117, B:G.118, A:G.118

8 x FMT: FORMIC ACID(Non-functional Binders)

FMT.6: 2 residues within 4Å: Chain A: R.282, A.285 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.282 Water bridges: A:R.282 FMT.7: 3 residues within 4Å: Chain A: W.256, W.275 Ligands: FMT.8 No protein-ligand interaction detected (PLIP) FMT.8: 4 residues within 4Å: Chain A: P.278, Q.279, R.282 Ligands: FMT.7 No protein-ligand interaction detected (PLIP) FMT.16: 4 residues within 4Å: Chain B: D.227, G.253, D.254, M.255 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.254 FMT.17: 4 residues within 4Å: Chain B: W.256, Q.279, R.282 Ligands: FMT.18 No protein-ligand interaction detected (PLIP) FMT.18: 4 residues within 4Å: Chain B: W.256, W.275, Q.279 Ligands: FMT.17 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:W.256 FMT.19: 6 residues within 4Å: Chain B: L.165, R.168, A.169, Y.210, N.270 Ligands: EDO.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.168, B:Y.210, B:Y.210, B:N.270 FMT.20: 5 residues within 4Å: Chain B: R.125, F.322, S.323, L.324, T.325 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.325 Water bridges: B:R.65

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chang, C. et al., Crystal structure of O-methyltransferase family 2 protein Plim_1147 from Planctomyces limnophilus DSM 3776 complex with Apigenin. To Be Published

Release Date

2016-03-02

Peptides

O-methyltransferase family 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

O-methyltransferase family 2