SMTL ID : 1qlb.1

respiratory complex II-like fumarate reductase from Wolinella succinogenes

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x FAD: FLAVIN-ADENINE DINUCLEOTIDE(Covalent)

FAD.1: 39 residues within 4Å: Chain A: I.11, G.12, G.13, G.14, L.15, A.16, L.34, S.35, L.36, I.37, S.42, H.43, S.44, A.46, A.47, Q.48, G.49, G.50, K.179, E.180, A.181, A.215, T.216, G.217, T.227, N.228, T.235, L.267, H.369, Y.370, G.392, E.393, R.404, G.407, N.408, S.409, V.410, A.413 Ligands: FUM.2 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:A.46 Hydrogen bonds: A:G.13, A:G.13, A:A.16, A:L.36, A:I.37, A:H.43, A:S.44, A:S.44, A:Q.48, A:G.49, A:G.50, A:G.50, A:A.181, A:A.181, A:G.217, A:T.235, A:E.393, A:R.404, A:G.407, A:S.409, A:V.410 Water bridges: A:G.14, A:G.14, A:E.393, A:E.393, A:A.394 pi-Cation interactions: A:H.369 FAD.10: 39 residues within 4Å: Chain D: I.11, G.12, G.13, G.14, L.15, A.16, L.34, S.35, L.36, I.37, S.42, H.43, S.44, A.46, A.47, Q.48, G.49, G.50, K.179, E.180, A.181, A.215, T.216, G.217, T.227, N.228, T.235, L.267, H.369, Y.370, G.392, E.393, R.404, G.407, N.408, S.409, V.410, A.413 Ligands: FUM.11 29 PLIP interactions: 29 interactions with chain D Hydrophobic interactions: D:A.46 Hydrogen bonds: D:G.13, D:G.13, D:A.16, D:L.36, D:I.37, D:H.43, D:S.44, D:S.44, D:Q.48, D:G.49, D:G.50, D:G.50, D:A.181, D:A.181, D:G.217, D:E.393, D:R.404, D:G.407, D:S.409, D:V.410 Water bridges: D:G.14, D:G.14, D:E.180, D:T.235, D:Y.370, D:E.393, D:E.393 pi-Cation interactions: D:H.369

2 x FUM: FUMARIC ACID(Non-covalent)

FUM.2: 9 residues within 4Å: Chain A: F.141, H.257, L.267, T.269, R.301, H.369, R.404, G.407 Ligands: FAD.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.141, A:L.267 Hydrogen bonds: A:G.407 Water bridges: A:G.49, A:R.404, A:R.404 Salt bridges: A:H.257, A:R.301, A:H.369, A:R.404 FUM.11: 9 residues within 4Å: Chain D: F.141, H.257, L.267, T.269, R.301, H.369, R.404, G.407 Ligands: FAD.10 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:F.141, D:L.267 Hydrogen bonds: D:G.407 Water bridges: D:G.49, D:R.404, D:R.404 Salt bridges: D:H.257, D:R.301, D:H.369, D:R.404

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: S.371, M.372, G.373, G.374, E.393, A.395 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:S.371, A:M.372, A:G.373, A:E.393, A:A.395, H2O.5 CA.12: 5 residues within 4Å: Chain D: S.371, M.372, G.373, E.393, A.395 6 PLIP interactions: 5 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:S.371, D:M.372, D:G.373, D:E.393, D:A.395, H2O.14

2 x FES: FE2/S2 (INORGANIC) CLUSTER(Non-covalent)

FES.4: 10 residues within 4Å: Chain B: F.55, V.56, C.57, R.58, G.60, I.61, C.62, G.63, C.65, C.77 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.57, B:C.62, B:C.65, B:C.77 FES.13: 10 residues within 4Å: Chain E: F.55, V.56, C.57, R.58, G.60, I.61, C.62, G.63, C.65, C.77 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.57, E:C.62, E:C.65, E:C.77

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

F3S.5: 11 residues within 4Å: Chain B: C.161, T.163, F.170, A.173, C.208, M.209, T.210, L.211, L.212, A.213, C.214 3 PLIP interactions: 3 interactions with chain B, Metal complexes: B:C.161, B:C.208, B:C.214 F3S.14: 11 residues within 4Å: Chain E: C.161, T.163, F.170, A.173, C.208, M.209, T.210, L.211, L.212, A.213, C.214 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Ligand interactions Metal complexes: E:C.161, E:C.208, E:C.214, F3S.14

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

SF4.6: 10 residues within 4Å: Chain B: F.111, C.151, I.152, E.153, C.154, G.155, C.157, C.218, P.219, K.220 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.151, B:C.154, B:C.157, B:C.218 SF4.15: 11 residues within 4Å: Chain E: F.111, C.151, I.152, E.153, C.154, G.155, C.156, C.157, C.218, P.219, K.220 4 PLIP interactions: 4 interactions with chain E, Metal complexes: E:C.151, E:C.154, E:C.157, E:C.218

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

HEM.7: 25 residues within 4Å: Chain C: Q.30, S.31, G.34, L.37, G.38, M.41, F.90, H.93, A.94, A.97, K.100, F.101, W.126, Q.129, G.133, M.136, F.137, V.179, H.182, G.183, G.186, L.187, L.190, K.193 Ligands: HEM.8 21 PLIP interactions: 21 interactions with chain C, Hydrophobic interactions: C:L.37, C:L.37, C:F.90, C:A.97, C:F.101, C:M.136, C:F.137, C:V.179, C:L.190 Hydrogen bonds: C:Q.30, C:W.126 Water bridges: C:Q.129, C:K.193 Salt bridges: C:K.100, C:K.193, C:K.193 pi-Stacking: C:H.93, C:H.182, C:H.182 Metal complexes: C:H.93, C:H.182 HEM.8: 20 residues within 4Å: Chain C: F.40, M.41, H.44, V.48, A.83, V.86, F.90, H.143, L.144, M.147, I.154, S.159, R.162, Y.172, L.175, L.176, G.224, T.227, F.228 Ligands: HEM.7 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:F.40, C:F.40, C:A.83, C:V.86, C:F.90, C:L.144, C:I.154, C:Y.172, C:Y.172, C:L.175, C:L.175 Salt bridges: C:R.162 pi-Stacking: C:H.44, C:H.44, C:H.143, C:H.143 Metal complexes: C:H.44, C:H.143 HEM.16: 25 residues within 4Å: Chain F: Q.30, S.31, G.34, L.37, G.38, M.41, F.90, H.93, A.94, A.97, K.100, F.101, W.126, Q.129, G.133, M.136, F.137, V.179, H.182, G.183, G.186, L.187, L.190, K.193 Ligands: HEM.17 22 PLIP interactions: 22 interactions with chain F, Hydrophobic interactions: F:L.37, F:L.37, F:F.90, F:A.97, F:F.101, F:M.136, F:F.137, F:V.179, F:L.190 Hydrogen bonds: F:Q.30, F:W.126 Water bridges: F:Q.129, F:K.193, F:K.193 Salt bridges: F:K.100, F:K.193, F:K.193 pi-Stacking: F:H.93, F:H.182, F:H.182 Metal complexes: F:H.93, F:H.182 HEM.17: 20 residues within 4Å: Chain F: F.40, M.41, H.44, V.48, A.83, V.86, F.90, H.143, L.144, M.147, I.154, S.159, R.162, Y.172, L.175, L.176, G.224, T.227, F.228 Ligands: HEM.16 19 PLIP interactions: 19 interactions with chain F, Hydrophobic interactions: F:F.40, F:F.40, F:A.83, F:V.86, F:F.90, F:L.144, F:I.154, F:Y.172, F:Y.172, F:L.175, F:L.175 Hydrogen bonds: F:Y.172 Salt bridges: F:R.162 pi-Stacking: F:H.44, F:H.44, F:H.143, F:H.143 Metal complexes: F:H.44, F:H.143

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

LMT.9: 12 residues within 4Å: Chain C: F.101, P.102, N.104, Y.105, Y.108, W.127, M.131 Chain F: M.22, L.26, F.95, M.98, R.99 9 PLIP interactions: 3 interactions with chain F, 6 interactions with chain C Hydrophobic interactions: F:F.95, F:F.95, F:R.99, C:F.101, C:P.102, C:Y.108, C:W.127, C:M.131 Hydrogen bonds: C:Y.105 LMT.18: 12 residues within 4Å: Chain C: M.22, L.26, F.95, M.98, R.99 Chain F: F.101, P.102, N.104, Y.105, Y.108, W.127, M.131 9 PLIP interactions: 6 interactions with chain F, 3 interactions with chain C Hydrophobic interactions: F:F.101, F:P.102, F:Y.108, F:W.127, F:M.131, C:F.95, C:F.95, C:R.99 Hydrogen bonds: F:Y.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lancaster, C.R.D. et al., Structure of Fumarate Reductase from Wolinella Succinogenes at 2.2 Angstroms Resolution. Nature (1999)

Release Date

1999-11-29

Peptides

FUMARATE REDUCTASE FLAVOPROTEIN SUBUNIT: AD
FUMARATE REDUCTASE IRON-SULFUR PROTEIN: BE
FUMARATE REDUCTASE CYTOCHROME B SUBUNIT: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
D

B
B

E
E

C
C

F
F

Membrane

We predict this structure to be a membrane protein.
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FUMARATE REDUCTASE FLAVOPROTEIN SUBUNIT

FUMARATE REDUCTASE IRON-SULFUR PROTEIN

FUMARATE REDUCTASE CYTOCHROME B SUBUNIT

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