SMTL ID : 3vrd.1

Crystal structure of flavocytochrome c from Thermochromatium tepidum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

hetero-1-1-mer

Ligands

2 x HEC: HEME C(Non-covalent)(Covalent)

HEC.1: 26 residues within 4Å: Chain A: C.11, C.14, H.15, P.27, I.29, M.32, F.37, V.40, M.41, F.44, S.51, T.52, I.53, M.54, I.57, Y.61, M.69, F.73, Y.128 Chain B: Y.306, L.334, T.336, Y.338, Y.387 Ligands: HEC.2, GOL.3 23 PLIP interactions: 18 interactions with chain A, 5 interactions with chain B, Hydrophobic interactions: A:I.29, A:I.29, A:F.37, A:F.37, A:V.40, A:F.44, A:F.44, A:I.53, A:I.57, A:F.73, B:L.334, B:T.336, B:Y.338, B:Y.387 Hydrogen bonds: A:T.52, A:I.53, A:M.54, B:Y.387 Water bridges: A:S.28, A:I.120, A:Q.124, A:Q.124 Metal complexes: A:H.15 HEC.2: 20 residues within 4Å: Chain A: Y.100, C.101, C.104, H.105, H.119, L.121, Y.128, A.132, I.133, F.136, R.141, P.142, E.144, K.146, M.147, K.150, L.154, L.166, Y.170 Ligands: HEC.1 21 PLIP interactions: 21 interactions with chain A, Hydrophobic interactions: A:Y.100, A:L.121, A:A.132, A:F.136, A:F.136, A:K.146, A:M.147, A:K.150, A:L.154 Water bridges: A:I.120, A:I.120, A:R.141, A:R.141, A:R.141, A:R.141, A:P.142 Salt bridges: A:R.141, A:R.141 pi-Stacking: A:H.119, A:F.136 Metal complexes: A:H.105

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: F.44, Y.128, A.132, D.135, R.141 Chain B: R.383 Ligands: HEC.1 7 PLIP interactions: 4 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Y.128, A:D.135, A:R.141, A:R.141, B:R.383 Water bridges: B:Y.387, B:Y.387 GOL.4: 6 residues within 4Å: Chain A: P.2, G.60, Y.61, S.62, D.65 Chain B: V.365 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.62 Water bridges: A:G.60, A:S.62, A:D.65, A:D.65 GOL.7: 4 residues within 4Å: Chain B: L.55, A.135, R.138, E.142 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.142 Water bridges: B:L.55, B:R.138

2 x NO3: NITRATE ION(Non-functional Binders)

NO3.5: 3 residues within 4Å: Chain A: R.137, K.152, L.155 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.137, A:R.137 NO3.8: 5 residues within 4Å: Chain B: L.207, A.342, P.343, G.344, Y.345 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.344

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

FAD.6: 33 residues within 4Å: Chain B: V.8, G.9, G.11, T.12, G.13, I.33, E.34, P.35, N.36, Y.39, C.42, Y.43, S.45, N.46, S.76, A.77, A.103, P.104, G.105, W.128, R.160, C.161, R.168, I.261, G.293, D.294, K.303, S.304, A.305, Y.306, A.308, Y.338, W.391 34 PLIP interactions: 34 interactions with chain B Hydrophobic interactions: B:W.128, B:W.128, B:R.160 Hydrogen bonds: B:G.11, B:T.12, B:T.12, B:G.13, B:N.36, B:Y.39, B:Y.43, B:A.77, B:A.77, B:G.105, B:D.294, B:K.303, B:A.305, B:Y.306 Water bridges: B:G.14, B:E.34, B:E.34, B:Y.39, B:C.42, B:R.160, B:R.160, B:R.160, B:K.260, B:I.261, B:I.261, B:I.261, B:D.294, B:A.295, B:Y.338, B:W.391 Salt bridges: B:R.160

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hirano, Y. et al., Structure Analysis and Comparative Characterization of the Cytochrome c' and Flavocytochrome c from Thermophilic Purple Photosynthetic Bacterium Thermochromatium tepidum. Biochemistry (2012)

Release Date

2012-09-12

Peptides

Flavocytochrome c heme subunit: A
Flavocytochrome c flavin subunit: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Flavocytochrome c heme subunit

Flavocytochrome c flavin subunit