SMTL ID : 1l9j.1 (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 Compare

Method

X-RAY DIFFRACTION 3.25 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 28 residues within 4Å: Chain A: F.97, A.124, I.125, A.127, Y.128, L.131, W.156, V.157, 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.2, BCL.6, BCL.7, BPH.8 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:F.97, A:A.127, A:Y.128, A:T.160, A:Y.162, A:F.167, A:F.167, A:A.176, A:I.177, A:F.180, A:F.181 Metal complexes: A:H.173 BCL.2: 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.1, BCL.7, BPH.8, U10.9, LDA.10 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B, Hydrophobic interactions: A:I.46, A:I.49, A:Y.128, A:L.131, A:F.146, A:L.154, B:F.197, B:I.206, B:L.214 Metal complexes: A:H.153 pi-Stacking: B:Y.210 BCL.6: 17 residues within 4Å: Chain A: H.168, M.174, I.177, S.178, F.181, T.182 Chain B: W.157, L.160, V.175, I.179, H.182, L.183, T.186 Ligands: BCL.1, BPH.3, BCL.7, LDA.11 10 PLIP interactions: 4 interactions with chain B, 6 interactions with chain A, Hydrophobic interactions: B:L.160, B:V.175, B:L.183, A:I.177, A:I.177, A:F.181 Metal complexes: B:H.182 Hydrogen bonds: A:T.182, A:T.182 pi-Stacking: A:F.181 BCL.7: 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, G.280, G.281, I.284 Ligands: BCL.1, BCL.2, BPH.3, BCL.6 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: 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, B:V.276 Metal complexes: B:H.202

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.3: 21 residues within 4Å: Chain A: F.181, A.184, L.185, L.189, L.219, V.220 Chain B: 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.6, BCL.7 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.185 pi-Stacking: B:F.150 BPH.8: 30 residues within 4Å: Chain A: A.42, I.46, I.49, I.89, C.92, A.93, A.96, F.97, W.100, E.104, I.117, A.120, F.121, A.124, Y.128, 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.1, BCL.2, U10.9 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:A.42, A:I.46, A:I.49, A:I.89, A:A.93, A:A.96, A:W.100, A:A.120, A:F.121, A:F.121, A:Y.148, A:L.238, A:V.241, A:V.241, B:A.213 pi-Stacking: A:F.121, A:F.121

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

FE2.4: 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.5: 1 residues within 4Å: Chain B: H.145 Ligand excluded by PLIP

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

U10.9: 21 residues within 4Å: Chain A: F.29, W.100 Chain B: L.214, M.218, H.219, T.222, I.223, 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.2, BPH.8 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.214, B:M.218, B:W.252, B:F.258, B:A.260, B:I.265, B:W.268, A:F.29, A:W.100, A:W.100 Hydrogen bonds: B:T.222, B:A.260

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

LDA.10: 9 residues within 4Å: Chain A: W.151 Chain B: P.200, L.204, A.207, F.208, M.272 Chain C: W.21, I.28 Ligands: BCL.2 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:W.21, C:I.28 LDA.11: 10 residues within 4Å: Chain B: F.67, F.74, M.122, W.157, V.175, P.176, Y.177, G.178, H.182 Ligands: BCL.6 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.67, B:F.67, B:F.74, B:V.175, B:H.182

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.12: 28 residues within 4Å: Chain A: Y.162 Chain B: L.191 Chain D: Q.14, C.15, C.18, H.19, T.36, P.38, L.40, V.43, R.46, A.48, G.49, F.54, Y.57, G.58, M.61, W.71, F.76, Y.79, V.80, G.98, K.99, M.100, T.101, F.102, L.104, I.113 25 PLIP interactions: 24 interactions with chain D, 1 interactions with chain A, Hydrophobic interactions: D:P.38, D:L.40, D:V.43, 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:F.102, D:F.102, D:L.104, D:I.113, A:Y.162 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, D:H.19 Metal complexes: D:H.19

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
L

B
M

C
H

D
C

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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