SMTL ID : 5tds.1

Toluene bound in the resting active site of toluene 4-monooxygenase (T4moH)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

hetero-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, MBN.6 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.104, A:E.134, A:H.137, H2O.2, H2O.2, H2O.8 FE.2: 6 residues within 4Å: Chain A: E.134, E.197, E.231, H.234 Ligands: FE.1, MBN.6 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.134, A:E.197, A:E.231, A:H.234, H2O.2, H2O.8 FE.14: 4 residues within 4Å: Chain D: E.104, E.134, H.137 Ligands: FE.15 6 PLIP interactions: 3 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.104, D:E.134, D:H.137, H2O.38, H2O.41, H2O.48 FE.15: 6 residues within 4Å: Chain D: E.134, E.197, E.231, H.234 Ligands: FE.14, MBN.20 6 PLIP interactions: 4 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.134, D:E.197, D:E.231, D:H.234, H2O.38, H2O.48

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

MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Chain B: E.298 No protein-ligand interaction detected (PLIP) MG.9: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.10: 1 residues within 4Å: Chain B: E.184 No protein-ligand interaction detected (PLIP) MG.11: 2 residues within 4Å: Chain B: D.40, K.56 No protein-ligand interaction detected (PLIP) MG.13: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain D: D.386, S.389 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.386, D:S.389, D:S.389, H2O.41, H2O.44 MG.22: 1 residues within 4Å: Chain E: T.36 No protein-ligand interaction detected (PLIP) MG.23: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

9 x MBN: TOLUENE(Non-covalent)

MBN.4: 14 residues within 4Å: Chain A: W.167, V.271, S.330, Y.331, G.334, V.335, W.338, P.394, I.402, P.403, V.405 Chain C: F.14, L.15 Ligands: MBN.5 12 PLIP interactions: 2 interactions with chain C, 10 interactions with chain A Hydrophobic interactions: C:F.14, C:L.15, A:W.167, A:V.271, A:Y.331, A:V.335, A:W.338, A:P.394, A:I.402, A:P.403, A:P.403, A:V.405 MBN.5: 11 residues within 4Å: Chain A: W.167, W.338, T.341, L.393, P.394, V.396, P.403, I.450, L.464, M.471 Ligands: MBN.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:W.167, A:W.167, A:W.338, A:T.341, A:L.393, A:P.394, A:V.396, A:I.450 MBN.6: 16 residues within 4Å: Chain A: I.100, G.103, E.104, A.107, E.134, Y.162, F.176, I.180, L.192, F.196, E.197, T.201, F.205 Ligands: FE.1, FE.2, MBN.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.100, A:F.176 pi-Stacking: A:F.196 MBN.7: 11 residues within 4Å: Chain A: I.100, F.196, F.200, T.201, Q.204, F.205, A.265, L.268, F.269, L.272 Ligands: MBN.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.201, A:F.269 pi-Stacking: A:F.196 MBN.12: 10 residues within 4Å: Chain A: M.3, W.9, P.56 Chain B: E.91, V.94, Q.95, F.98, T.164, H.165, Y.168 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:V.94, B:Y.168, B:Y.168, A:W.9, A:P.56, A:P.56 pi-Stacking: B:F.98 MBN.17: 14 residues within 4Å: Chain D: W.167, V.271, S.330, Y.331, G.334, V.335, W.338, P.394, I.402, P.403, V.405 Chain F: F.14, L.15 Ligands: MBN.18 11 PLIP interactions: 9 interactions with chain D, 2 interactions with chain F Hydrophobic interactions: D:W.167, D:V.271, D:Y.331, D:W.338, D:P.394, D:I.402, D:P.403, D:P.403, D:V.405, F:F.14, F:L.15 MBN.18: 11 residues within 4Å: Chain D: W.167, W.338, T.341, L.393, P.394, V.396, P.403, I.450, L.464, M.471 Ligands: MBN.17 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:W.167, D:W.167, D:W.167, D:W.338, D:T.341, D:L.393, D:P.394, D:V.396, D:I.450 MBN.20: 15 residues within 4Å: Chain D: I.100, G.103, E.104, A.107, E.134, Y.162, F.176, I.180, L.192, F.196, E.197, T.201, F.205 Ligands: FE.15, MBN.21 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:I.100, D:F.176, D:F.176 pi-Stacking: D:F.196 MBN.21: 11 residues within 4Å: Chain D: I.100, F.196, F.200, T.201, Q.204, F.205, A.265, L.268, F.269, L.272 Ligands: MBN.20 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:Q.204, D:L.268, D:F.269 pi-Stacking: D:F.196

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

CL.19: 4 residues within 4Å: Chain D: R.339, K.481, D.482, F.486 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Acheson, J.F. et al., In-crystal reaction cycle of a toluene-bound diiron hydroxylase. Nature (2017)

Release Date

2017-03-22

Peptides

Toluene-4-monooxygenase system protein A: AD
Toluene-4-monooxygenase system protein E: BE
Toluene-4-monooxygenase system protein B: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

Toluene-4-monooxygenase system protein A

Toluene-4-monooxygenase system protein E

Toluene-4-monooxygenase system protein B

Related Entries With Identical Sequence