SMTL ID : 1l9j.2 (1 other biounit)

X-Ray Structure of the Cytochrome-c(2)-Photosynthetic Reaction Center Electron Transfer Complex from Rhodobacter sphaeroides in Type I Co-Crystals

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.25 Å

Oligo State

hetero-oligomer

Ligands

1 x FE2: FE (II) ION(Non-covalent)

FE2.1: 5 residues within 4Å: Chain A: H.190, H.230 Chain B: H.219, E.234, H.266 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:H.219, B:E.234, B:H.266, A:H.190, A:H.230

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

CL.2: 2 residues within 4Å: Chain B: H.145, R.267 Ligand excluded by PLIP

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.3: 16 residues within 4Å: Chain A: H.168, M.174, I.177, S.178, F.181, T.182 Chain B: W.157, L.160, I.179, H.182, L.183, T.186 Ligands: BCL.4, BCL.5, BPH.7, LDA.12 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:I.177, A:I.177, B:L.160, B:L.183 Hydrogen bonds: A:T.182, A:T.182 pi-Stacking: A:F.181 Metal complexes: B:H.182 BCL.4: 29 residues within 4Å: Chain A: F.97, A.124, I.125, A.127, Y.128, L.131, W.156, V.157, S.158, T.160, G.161, Y.162, N.166, F.167, H.168, H.173, A.176, I.177, F.180, F.181, S.244, A.245, C.247, M.248 Chain B: Y.210 Ligands: BCL.3, BCL.5, BCL.6, BPH.8 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:F.97, A:F.97, A:A.124, A:A.127, A:Y.128, A:V.157, A:T.160, A:Y.162, A:F.167, A:A.176, A:I.177, A:F.180, A:F.181 Metal complexes: A:H.173 BCL.5: 26 residues within 4Å: Chain A: V.157, Y.162, F.181 Chain B: W.66, A.153, L.156, W.157, T.186, N.187, F.189, S.190, L.196, F.197, H.202, S.205, I.206, L.209, Y.210, V.276, T.277, G.280, I.284 Ligands: BCL.3, BCL.4, BCL.6, BPH.7 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:W.66, B:W.66, B:L.156, B:T.186, B:F.189, B:L.196, B:F.197, B:F.197, B:I.206, B:I.206, B:L.209, B:Y.210 pi-Stacking: B:F.197 Metal complexes: B:H.202 BCL.6: 20 residues within 4Å: Chain A: I.46, I.49, Y.128, L.131, F.146, I.150, W.151, H.153, L.154 Chain B: F.197, G.203, I.206, A.207, Y.210, L.214 Ligands: BCL.4, BCL.5, BPH.8, U10.9, LDA.11 9 PLIP interactions: 3 interactions with chain B, 6 interactions with chain A, Hydrophobic interactions: B:F.197, B:I.206, B:L.214, A:I.49, A:Y.128, A:L.131, A:F.146, A:L.154 Metal complexes: A:H.153

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.7: 21 residues within 4Å: Chain A: F.181, A.184, L.185, L.189, L.219 Chain B: S.59, L.60, G.63, L.64, A.125, V.126, W.129, T.146, A.149, F.150, A.153, A.273, V.274, T.277 Ligands: BCL.3, BCL.5 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.60, B:L.64, B:A.125, B:W.129, B:A.149, B:F.150, B:F.150, B:T.277, A:A.184, A:L.189 pi-Stacking: B:F.150 BPH.8: 30 residues within 4Å: Chain A: T.38, A.42, I.49, C.92, A.93, A.96, F.97, W.100, E.104, I.117, A.120, F.121, A.124, Y.128, F.146, Y.148, G.149, I.150, H.153, L.238, V.241 Chain B: Y.210, A.213, L.214, M.218, W.252, M.256 Ligands: BCL.4, BCL.6, U10.9 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.38, A:A.42, A:I.49, A:A.96, A:A.120, A:F.121, A:F.121, A:A.124, A:F.146, A:Y.148, A:Y.148, A:Y.148, A:L.238, A:V.241, A:V.241, B:A.213, B:L.214 pi-Stacking: A:F.121

1 x U10: UBIQUINONE-10(Non-covalent)

U10.9: 19 residues within 4Å: Chain A: W.100 Chain B: L.214, M.218, H.219, T.222, A.248, A.249, W.252, M.256, F.258, N.259, A.260, T.261, M.262, I.265, W.268, M.272 Ligands: BCL.6, BPH.8 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:L.214, B:M.218, B:W.252, B:M.256, B:F.258, B:F.258, B:A.260, B:I.265, B:W.268, B:W.268 Hydrogen bonds: B:T.222, B:A.260

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.10: 25 residues within 4Å: Chain B: L.191 Chain D: Q.14, C.15, C.18, H.19, T.36, P.38, R.46, A.48, G.49, F.54, G.56, Y.57, G.58, M.61, W.71, F.76, Y.79, V.80, K.99, M.100, T.101, F.102, L.104, I.113 20 PLIP interactions: 19 interactions with chain D, 1 interactions with chain B, Hydrophobic interactions: D:T.36, D:F.54, D:W.71, D:F.76, D:F.76, D:Y.79, D:V.80, D:F.102, D:F.102, D:L.104, D:I.113, B:L.191 Hydrogen bonds: D:G.49, D:G.58, D:K.99 Salt bridges: D:R.46 pi-Stacking: D:H.19, D:H.19 pi-Cation interactions: D:H.19 Metal complexes: D:H.19

2 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)

LDA.11: 9 residues within 4Å: Chain A: W.151 Chain B: P.200, L.204, A.207, F.208, W.268 Chain C: W.21, I.28 Ligands: BCL.6 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.204, B:A.207, B:W.268, C:W.21 LDA.12: 9 residues within 4Å: Chain B: F.67, F.74, M.122, V.175, P.176, Y.177, G.178, H.182 Ligands: BCL.3 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.67, B:F.74, B:V.175, B:H.182 pi-Cation interactions: B:Y.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Axelrod, H.L. et al., X-ray structure determination of the cytochrome c2: reaction center electron transfer complex from Rhodobacter sphaeroides. J.Mol.Biol. (2002)

Release Date

2002-06-12

Peptides

REACTION CENTER PROTEIN L CHAIN: A
REACTION CENTER PROTEIN M CHAIN: B
REACTION CENTER PROTEIN H CHAIN: C
cytochrome c-2: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
R

B
S

C
T

D
D

Membrane

We predict this structure to be a membrane protein.
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REACTION CENTER PROTEIN L CHAIN

REACTION CENTER PROTEIN M CHAIN

REACTION CENTER PROTEIN H CHAIN

cytochrome c-2

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