SMTL ID : 3dhh.1

Crystal Structure of Resting State Toluene 4-Monoxygenase Hydroxylase Complexed with Effector Protein

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

hetero-2-2-2-2-mer

Ligands

4 x FE: FE (III) ION(Non-covalent)

FE.1: 5 residues within 4Å: Chain A: E.104, E.134, H.137 Ligands: FE.2, 1PE.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.104, A:E.134, A:H.137, H2O.1, H2O.1 FE.2: 6 residues within 4Å: Chain A: E.134, E.197, E.231, H.234 Ligands: FE.1, 1PE.5 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.134, A:E.197, A:E.231, A:H.234, H2O.1 FE.11: 5 residues within 4Å: Chain E: E.104, E.134, H.137 Ligands: FE.12, 1PE.15 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:E.104, E:E.134, E:H.137, H2O.30, H2O.30 FE.12: 6 residues within 4Å: Chain E: E.134, E.197, E.231, H.234 Ligands: FE.11, 1PE.15 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:E.134, E:E.197, E:E.231, E:H.234, H2O.30

10 x BML: 4-BROMOPHENOL(Non-covalent)

BML.3: 11 residues within 4Å: Chain A: W.167, S.330, G.334, V.335, W.338, T.341, P.394, P.403, V.405 Chain C: F.14 Ligands: BML.7 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:V.335, A:W.338, A:W.338, A:P.394, A:P.403 Hydrogen bonds: A:W.167 Water bridges: A:T.341 pi-Stacking: A:W.167 BML.4: 8 residues within 4Å: Chain A: W.338, E.391, T.392, L.393, F.454, T.463, L.464 Ligands: BML.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.393, A:F.454 Hydrogen bonds: A:L.464 BML.7: 10 residues within 4Å: Chain A: W.167, L.393, P.394, V.396, Q.401, I.402, P.403, I.450 Ligands: BML.3, BML.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:W.167, A:W.167, A:P.394, A:V.396, A:P.403, A:I.450 BML.9: 8 residues within 4Å: Chain A: M.3, P.56 Chain B: E.91, Q.95, F.98, T.164, H.165, Y.168 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Q.95, B:Y.168, A:P.56 Hydrogen bonds: B:E.91, B:H.165 pi-Stacking: B:F.98, B:Y.168 BML.10: 10 residues within 4Å: Chain A: R.6, Y.51, K.52 Chain D: M.74, Q.75, E.78, L.81, A.90, D.91, I.95 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain D Hydrophobic interactions: A:Y.51, D:A.90 Hydrogen bonds: A:R.6, A:R.6, D:Q.75 Water bridges: A:K.52, D:A.90 BML.13: 11 residues within 4Å: Chain E: W.167, S.330, G.334, V.335, W.338, T.341, P.394, P.403, V.405 Chain G: F.14 Ligands: BML.17 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:V.335, E:W.338, E:W.338, E:P.394, E:P.403 Hydrogen bonds: E:W.167, E:T.341 pi-Stacking: E:W.167 BML.14: 8 residues within 4Å: Chain E: W.338, E.391, T.392, L.393, F.454, T.463, L.464 Ligands: BML.17 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:L.393, E:F.454 Hydrogen bonds: E:L.464 BML.17: 10 residues within 4Å: Chain E: W.167, L.393, P.394, V.396, Q.401, I.402, P.403, I.450 Ligands: BML.13, BML.14 6 PLIP interactions: 6 interactions with chain E Hydrophobic interactions: E:W.167, E:W.167, E:P.394, E:V.396, E:P.403, E:I.450 BML.19: 8 residues within 4Å: Chain E: M.3, P.56 Chain F: E.91, Q.95, F.98, T.164, H.165, Y.168 6 PLIP interactions: 1 interactions with chain E, 5 interactions with chain F Hydrophobic interactions: E:P.56, F:Q.95, F:Y.168 Hydrogen bonds: F:E.91 pi-Stacking: F:F.98, F:Y.168 BML.20: 10 residues within 4Å: Chain E: R.6, Y.51, K.52 Chain H: M.74, Q.75, E.78, L.81, A.90, D.91, I.95 7 PLIP interactions: 3 interactions with chain H, 4 interactions with chain E Hydrophobic interactions: H:A.90, E:Y.51 Hydrogen bonds: H:Q.75, E:R.6, E:R.6 Water bridges: H:A.90, E:K.52

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.5: 13 residues within 4Å: Chain A: A.99, I.100, G.103, E.104, A.107, E.134, Y.162, F.176, F.196, E.197, E.231 Ligands: FE.1, FE.2 No protein-ligand interaction detected (PLIP) 1PE.15: 13 residues within 4Å: Chain E: A.99, I.100, G.103, E.104, A.107, E.134, Y.162, F.176, F.196, E.197, E.231 Ligands: FE.11, FE.12 No protein-ligand interaction detected (PLIP)

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 3 residues within 4Å: Chain A: W.315 Chain E: W.435 Ligands: CL.16 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain A: W.435 Chain E: W.315 Ligands: CL.6 Ligand excluded by PLIP

2 x BTB: 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-covalent)

BTB.8: 5 residues within 4Å: Chain A: E.214, S.287 Chain D: D.44, R.45, R.46 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:S.287, D:R.45, D:R.46, D:R.46 Water bridges: A:E.214, A:E.214, A:E.214 Salt bridges: A:E.214 BTB.18: 5 residues within 4Å: Chain E: E.214, S.287 Chain H: D.44, R.45, R.46 6 PLIP interactions: 3 interactions with chain H, 3 interactions with chain E Hydrogen bonds: H:R.45, H:R.46, H:R.46, E:S.287 Water bridges: E:E.214 Salt bridges: E:E.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bailey, L.J. et al., Structural consequences of effector protein complex formation in a diiron hydroxylase. Proc.Natl.Acad.Sci.USA (2008)

Release Date

2008-12-30

Peptides

toluene 4-monooxygenase hydroxylase alpha subunit: AE
toluene 4-monooxygenase hydroxylase beta subunit: BF
toluene 4-monooxygenase hydroxylase gamma subunit: CG
Toluene-4-monooxygenase system effector protein: DH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

E
A

B
B

F
B

C
C

G
C

D
E

H
E

toluene 4-monooxygenase hydroxylase alpha subunit

toluene 4-monooxygenase hydroxylase beta subunit

toluene 4-monooxygenase hydroxylase gamma subunit

Toluene-4-monooxygenase system effector protein

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