SMTL ID : 2ivf.1

ETHYLBENZENE DEHYDROGENASE FROM AROMATOLEUM AROMATICUM

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

hetero-oligomer

Ligands

1 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.1: 7 residues within 4Å: Chain A: Q.111, P.113, F.670, E.765, Q.767, T.768, R.769 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.767, A:R.769 Water bridges: A:T.768 Salt bridges: A:R.769

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 8 residues within 4Å: Chain A: W.87, H.192, I.221, D.223, W.481 Ligands: MO.9, MGD.10, MD1.11 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.481 Salt bridges: A:H.192 ACT.7: 4 residues within 4Å: Chain A: L.771, S.772, E.785, V.786 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.785 Hydrogen bonds: A:V.786 Water bridges: A:M.773

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 9 residues within 4Å: Chain A: C.115, Y.122, S.240, D.242, P.669, R.769, V.788, K.790, P.791 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.122, A:S.240, A:D.242, A:R.769 Water bridges: A:C.115 GOL.4: 13 residues within 4Å: Chain A: T.224, M.226, A.449, S.451, Y.452, H.453, G.454, D.455, K.941, H.944, A.962, V.964, T.965 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.452, A:G.454, A:D.455 Water bridges: A:M.226, A:A.962 GOL.5: 12 residues within 4Å: Chain A: M.226, H.230, W.587, Y.821, L.943, H.944, A.946, F.952, R.953, G.959, S.960 Ligands: GOL.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.230, A:L.943, A:R.953, A:S.960 GOL.6: 8 residues within 4Å: Chain A: W.586, W.587, A.946, G.947, F.952, R.953, Y.954 Ligands: GOL.5 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:A.946, A:Y.954 Water bridges: A:W.586, A:H.591, A:Y.954 GOL.12: 8 residues within 4Å: Chain B: I.222, A.223, R.228, W.337, F.344, T.345, N.346, D.347 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:A.223, B:R.228, B:F.344, B:D.347, B:D.347 Water bridges: A:Q.111 GOL.14: 7 residues within 4Å: Chain B: N.141, G.280, F.281, T.288, K.290, T.291, R.292 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.280, B:T.288, B:T.288 Water bridges: B:R.292 GOL.19: 7 residues within 4Å: Chain B: K.185, G.186, R.188, Q.206 Chain C: F.89, V.90, K.121 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:R.188, C:V.90, C:V.90, C:K.121 Water bridges: B:K.185, C:K.121 GOL.20: 7 residues within 4Å: Chain B: H.189, E.192 Chain C: F.45, L.48, S.49, R.197, R.200 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:R.197, C:R.197, C:R.200, B:H.189 Water bridges: C:E.50

4 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.8: 12 residues within 4Å: Chain A: S.81, H.82, N.84, C.86, G.90, S.91, C.92, F.94, G.126, C.127, G.130, I.854 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:H.82, A:C.86, A:C.92, A:C.127 SF4.16: 13 residues within 4Å: Chain B: C.151, N.152, H.153, C.154, P.157, A.158, C.159, V.177, C.194, Y.196, A.198, I.199, K.210 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.151, B:C.154, B:C.159, B:C.194 SF4.17: 13 residues within 4Å: Chain B: C.28, L.29, G.30, C.31, Q.32, T.33, C.34, V.56, A.148, C.230, P.231, V.234, R.235 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.28, B:C.31, B:C.34, B:C.230 SF4.18: 12 residues within 4Å: Chain B: C.38, W.42, W.53, N.54, M.150, C.211, I.212, L.213, C.214, N.224, A.225, C.226 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.38, B:C.211, B:C.214, B:C.226

1 x MO: MOLYBDENUM ATOM(Non-covalent)

MO.9: 6 residues within 4Å: Chain A: I.221, D.223, H.849 Ligands: ACT.2, MGD.10, MD1.11 Ligand excluded by PLIP

1 x MGD: 2-AMINO-5,6-DIMERCAPTO-7-METHYL-3,7,8A,9-TETRAHYDRO-8-OXA-1,3,9,10-TETRAAZA-ANTHRACEN-4-ONE GUANOSINE DINUCLEOTIDE(Non-covalent)

MGD.10: 36 residues within 4Å: Chain A: I.85, C.86, W.87, K.129, D.223, T.253, C.254, S.255, N.256, Y.259, T.260, I.281, A.282, P.283, D.284, N.286, V.298, V.300, G.301, D.303, G.445, F.446, S.447, T.846, G.847, G.848, H.849, P.850, R.851, S.853, I.854, H.855, R.967 Ligands: ACT.2, MO.9, MD1.11 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:W.87, A:K.129, A:T.253, A:C.254, A:N.256, A:T.260, A:I.281, A:I.281, A:D.284, A:N.286, A:G.301, A:F.446, A:S.447, A:S.447, A:H.849, A:R.851, A:H.855 Water bridges: A:Q.128, A:S.255, A:Y.443, A:H.849, A:R.967 Salt bridges: A:D.303, A:R.967

1 x MD1: PHOSPHORIC ACID 4-(2-AMINO-4-OXO-3,4,5,6,-TETRAHYDRO-PTERIDIN-6-YL)-2-HYDROXY-3,4-DIMERCAPTO-BUT-3-EN-YL ESTER GUANYLATE ESTER(Non-covalent)

MD1.11: 36 residues within 4Å: Chain A: H.192, H.194, A.195, I.221, D.223, K.450, S.607, Q.608, N.609, R.612, R.613, R.615, L.635, E.636, T.637, R.638, S.640, C.652, A.653, W.654, Y.655, K.658, E.687, H.849, H.855, S.856, T.857, F.920, Y.932, D.933, L.936, D.966, R.967 Ligands: ACT.2, MO.9, MGD.10 40 PLIP interactions: 40 interactions with chain A Hydrogen bonds: A:N.609, A:N.609, A:R.612, A:R.612, A:R.613, A:L.635, A:T.637, A:T.637, A:T.637, A:R.638, A:A.653, A:K.658, A:H.855, A:S.856, A:S.856, A:T.857, A:Y.932, A:Y.932, A:R.967, A:R.967 Water bridges: A:K.450, A:S.607, A:Q.608, A:E.636, A:G.848, A:F.920, A:D.933, A:D.933 Salt bridges: A:H.194, A:H.194, A:R.612, A:R.612, A:R.613, A:E.636, A:E.687, A:H.855, A:D.933, A:D.966 pi-Stacking: A:F.920 pi-Cation interactions: A:R.612

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.13: 4 residues within 4Å: Chain B: H.314, R.317, E.318, R.321 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:H.314, B:E.318 Salt bridges: B:H.314, B:R.317, B:R.321

1 x F3S: FE3-S4 CLUSTER(Non-covalent)

F3S.15: 11 residues within 4Å: Chain B: C.163, T.165, I.168, C.184, K.185, G.186, H.187, R.188, H.189, C.190, S.208 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.163, B:C.184, B:C.190

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.21: 25 residues within 4Å: Chain B: T.165, K.185, H.187 Chain C: T.34, P.35, L.46, G.94, M.96, A.105, V.106, M.108, Y.119, I.130, F.135, V.138, R.140, A.186, F.187, A.188, W.190, S.198, G.199, K.201, Y.203, G.205 23 PLIP interactions: 19 interactions with chain C, 4 interactions with chain B, Hydrophobic interactions: C:T.34, C:P.35, C:L.46, C:M.96, C:A.105, C:Y.119, C:Y.119, C:I.130, C:V.138, C:V.138, C:A.186, C:A.188, C:Y.203, C:Y.203 Hydrogen bonds: C:Y.119 Water bridges: C:V.138, C:R.140 Salt bridges: C:R.140, B:K.185, B:K.185, B:H.187, B:H.187 pi-Stacking: C:W.190

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kloer, D.P. et al., Crystal Structure of Ethylbenzene Dehydrogenase from Aromatoleum Aromaticum. Structure (2006)

Release Date

2006-09-14

Peptides

ETHYLBENZENE DEHYDROGENASE ALPHA-SUBUNIT: A
ETHYLBENZENE DEHYDROGENASE BETA-SUBUNIT: B
ETHYLBENZENE DEHYDROGENASE GAMMA-SUBUNIT: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

ETHYLBENZENE DEHYDROGENASE ALPHA-SUBUNIT

ETHYLBENZENE DEHYDROGENASE BETA-SUBUNIT

ETHYLBENZENE DEHYDROGENASE GAMMA-SUBUNIT