SMTL ID : 1l9b.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NA: SODIUM ION(Non-functional Binders)

NA.1: 2 residues within 4Å: Chain A: W.266 Chain B: F.90 No protein-ligand interaction detected (PLIP)

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.2: 26 residues within 4Å: Chain A: F.97, A.124, Y.128, L.131, V.157, T.160, G.161, Y.162, N.166, F.167, H.168, H.173, A.176, I.177, F.180, S.244, A.245, C.247, M.248 Chain B: Y.210 Ligands: BCL.3, BCL.12, BCL.13, BPH.14, U10.15, LDA.20 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:F.97, A:F.97, A:Y.128, A:V.157, A:T.160, A:Y.162, A:F.167, A:A.176, A:I.177, A:I.177, A:F.180 Metal complexes: A:H.173 BCL.3: 21 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.2, LDA.6, BCL.13, BPH.14, U10.15, LDA.17 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B, Hydrophobic interactions: A:I.46, A:I.49, A:F.146, A:L.154, B:F.197, B:I.206, B:I.206, B:L.214 Metal complexes: A:H.153 pi-Stacking: B:Y.210 BCL.12: 15 residues within 4Å: Chain A: H.168, M.174, I.177, S.178, F.181, T.182 Chain B: W.157, I.179, H.182, L.183, T.186 Ligands: BCL.2, BPH.4, BCL.13, LDA.18 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, Hydrophobic interactions: B:L.183, A:I.177, A:I.177 Metal complexes: B:H.182 BCL.13: 27 residues within 4Å: Chain A: V.157, Y.162, F.181 Chain B: A.153, L.156, W.157, L.160, 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, G.281, I.284 Ligands: BCL.2, BCL.3, BPH.4, BCL.12 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:L.156, B:T.186, B:F.189, B:L.196, B:F.197, B:F.197, B:I.206, B:L.209, B:Y.210, B:V.276, B:T.277 Metal complexes: B:H.202

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.4: 22 residues within 4Å: Chain A: F.181, A.184, L.185, L.189, L.219, V.220 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.12, BCL.13 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.60, B:L.64, B:A.125, B:A.149, B:F.150, B:A.153, B:T.277, A:A.184, A:L.185 pi-Stacking: B:F.150 BPH.14: 27 residues within 4Å: Chain A: F.41, A.42, I.46, I.49, A.93, F.97, W.100, E.104, I.117, A.120, F.121, A.124, Y.148, H.153, S.237, L.238, V.241 Chain B: Y.210, A.213, L.214, M.218, W.252, M.256 Ligands: BCL.2, BCL.3, LDA.6, U10.15 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.42, A:I.46, A:I.49, A:A.120, A:F.121, A:F.121, A:Y.148, A:Y.148, A:L.238, A:V.241, A:V.241, B:Y.210, B:A.213, B:L.214 pi-Stacking: A:F.121

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

LDA.5: 3 residues within 4Å: Chain A: W.59, I.64 Ligands: LDA.6 No protein-ligand interaction detected (PLIP) LDA.6: 6 residues within 4Å: Chain A: I.49, P.61, I.64 Ligands: BCL.3, LDA.5, BPH.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.64, A:I.150 LDA.7: 6 residues within 4Å: Chain A: V.98, A.101, V.105, Y.115, P.118, F.119 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.101 LDA.8: 4 residues within 4Å: Chain A: P.171, W.262, W.263, W.265 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.171, A:W.262, A:W.262, A:W.263, A:W.265, A:W.265 Water bridges: A:W.262 LDA.16: 9 residues within 4Å: Chain B: W.148, S.152, W.155, R.267, I.270, W.271, L.278 Chain C: Y.30 Ligands: CL.11 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:W.155, B:I.270, B:W.271, B:L.278 Hydrogen bonds: C:Y.30, C:Y.30 LDA.17: 7 residues within 4Å: Chain B: P.200, L.204, A.207, F.208 Chain C: W.21, I.28 Ligands: BCL.3 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:W.21, C:I.28, B:F.208 LDA.18: 11 residues within 4Å: Chain B: F.67, I.70, F.74, M.122, W.157, V.175, P.176, Y.177, G.178, H.182 Ligands: BCL.12 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.67, B:F.67, B:F.74, B:Y.177, B:H.182 Hydrogen bonds: B:Y.177 LDA.19: 5 residues within 4Å: Chain C: M.175, A.176, M.193, Q.194 Ligands: HTO.9 No protein-ligand interaction detected (PLIP) LDA.20: 3 residues within 4Å: Chain C: W.21 Ligands: BCL.2, U10.15 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:W.21, C:W.21 pi-Cation interactions: C:W.21

2 x HTO: HEPTANE-1,2,3-TRIOL(Non-covalent)

HTO.9: 4 residues within 4Å: Chain A: H.116, R.231 Chain B: S.227 Ligands: LDA.19 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.231, B:S.227, B:S.227 HTO.22: 8 residues within 4Å: Chain A: D.155, N.159 Chain B: N.195 Chain D: Q.16, T.17, R.32, N.33, A.34 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D, 2 interactions with chain A Hydrogen bonds: B:N.195, D:R.32 Water bridges: B:Y.198, A:D.155 Hydrophobic interactions: A:D.155

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

FE2.10: 5 residues within 4Å: Chain A: H.190, H.230 Chain B: H.219, E.234, H.266 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Metal complexes: A:H.190, A:H.230, B:H.219, B:E.234, B:H.266

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

CL.11: 3 residues within 4Å: Chain B: H.145, R.267 Ligands: LDA.16 Ligand excluded by PLIP

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

U10.15: 22 residues within 4Å: Chain A: 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, BCL.3, BPH.14, LDA.20 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.214, B:M.218, B:H.219, B:W.252, B:F.258, B:F.258, B:A.260, B:I.265, B:W.268, B:W.268 Hydrogen bonds: B:A.260

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Covalent)

HEM.21: 27 residues within 4Å: Chain A: Y.162 Chain B: L.191 Chain D: Q.14, C.15, C.18, H.19, T.36, G.37, 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 29 PLIP interactions: 27 interactions with chain D, 1 interactions with chain B, 1 interactions with chain A, Hydrophobic interactions: D:P.38, D:F.54, D:W.71, D:F.76, D:F.76, D:V.80, D:K.99, D:F.102, D:F.102, D:F.102, D:L.104, D:I.113, B:L.191, A:Y.162 Hydrogen bonds: D:G.49, D:G.58, D:K.99 Water bridges: D:R.46, D:T.50, D:M.61, D:Y.79, D:Y.79 Salt bridges: D:R.46 pi-Stacking: D:H.19, D:H.19, D:H.19, D:Y.79 pi-Cation interactions: 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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