SMTL ID : 6sek.1

Crystal Structure of Ancestral Flavin-containing monooxygenase (FMO) 5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

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

FAD.1: 32 residues within 4Å: Chain A: I.9, G.10, A.11, G.12, A.13, S.14, F.32, E.33, R.34, T.35, G.39, G.40, L.41, W.42, G.51, R.52, I.61, N.62, T.63, T.109, T.110, V.111, C.147, T.148, G.149, H.151, F.338, G.376, A.377, I.378, M.379 Ligands: NAP.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:L.41, A:H.151 Hydrogen bonds: A:G.10, A:G.12, A:S.14, A:S.14, A:R.34, A:R.34, A:G.39, A:L.41, A:W.42, A:N.62, A:T.63, A:T.63, A:V.111, A:V.111, A:H.151, A:I.378 pi-Stacking: A:W.42 FAD.7: 31 residues within 4Å: Chain B: I.9, G.10, G.12, A.13, S.14, F.32, E.33, R.34, T.35, G.39, G.40, L.41, W.42, G.51, R.52, I.61, N.62, T.63, T.109, T.110, V.111, C.147, T.148, G.149, H.151, F.338, G.376, A.377, I.378, M.379 Ligands: NAP.8 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:L.41 Hydrogen bonds: B:G.10, B:A.11, B:G.12, B:S.14, B:S.14, B:S.14, B:R.34, B:R.34, B:T.35, B:G.39, B:G.40, B:L.41, B:W.42, B:N.62, B:T.63, B:T.63, B:T.63, B:V.111, B:V.111, B:G.149, B:H.151, B:I.378 pi-Stacking: B:W.42

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.2: 27 residues within 4Å: Chain A: Y.56, I.60, I.61, N.62, H.151, H.155, P.157, S.160, F.161, I.191, G.192, I.193, G.194, N.195, S.196, D.199, R.216, R.217, H.282, N.303, A.329, T.330, G.331, Q.373, S.423, R.425 Ligands: FAD.1 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:N.195 Hydrogen bonds: A:I.60, A:N.62, A:S.160, A:S.160, A:I.193, A:G.194, A:N.195, A:N.195, A:S.196, A:S.196, A:R.216, A:H.282, A:G.331, A:Q.373, A:Q.373, A:S.423 Water bridges: A:G.197, A:G.197 Salt bridges: A:R.216, A:R.217, A:R.425, A:R.425 pi-Cation interactions: A:R.216, A:R.216 NAP.8: 29 residues within 4Å: Chain B: Y.56, V.59, I.60, I.61, N.62, H.151, H.155, P.157, S.160, F.161, I.191, G.192, I.193, G.194, N.195, S.196, G.197, D.199, R.216, R.217, H.282, A.329, T.330, G.331, Y.332, Q.373, S.423, R.425 Ligands: FAD.7 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:N.195 Hydrogen bonds: B:I.60, B:N.62, B:S.160, B:S.160, B:I.193, B:G.194, B:N.195, B:S.196, B:S.196, B:G.197, B:R.216, B:H.282, B:Q.373, B:Q.373, B:S.423 Salt bridges: B:R.216, B:R.217, B:R.425, B:R.425 pi-Cation interactions: B:R.216, B:R.216

1 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.3: 11 residues within 4Å: Chain A: D.227, V.234, L.235, F.236, S.238, F.240, T.241, F.256, K.260, F.465 Chain B: Q.263 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.235, A:S.238, A:S.238 Salt bridges: A:K.260

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.4: 6 residues within 4Å: Chain A: S.245, K.246, L.257, L.279, D.431, D.434 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.245, A:D.431 Salt bridges: A:K.246, A:D.431, A:D.434 EPE.9: 4 residues within 4Å: Chain B: Y.242, S.245, D.431, D.434 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.245, B:D.434 Salt bridges: B:D.431, B:D.434

2 x GLC: alpha-D-glucopyranose(Non-covalent)

GLC.5: 1 residues within 4Å: Chain A: I.247 No protein-ligand interaction detected (PLIP) GLC.6: 8 residues within 4Å: Chain A: Q.170, F.172, D.176, Y.177, K.178, N.179, G.182, F.183 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.170, A:Q.170, A:K.178, A:N.179, A:N.179, A:N.179, A:G.182

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nicoll, C.R. et al., Ancestral-sequence reconstruction unveils the structural basis of function in mammalian FMOs. Nat.Struct.Mol.Biol. (2020)

Release Date

2019-12-25

Peptides

Ancestral Flavin-containing monooxygenase 5: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Ancestral Flavin-containing monooxygenase 5