SMTL ID : 3i4d.1

Photosynthetic reaction center from rhodobacter sphaeroides 2.4.1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

hetero-oligomer

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, S.158, 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.2, BPH.3, BCL.36, BCL.37 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:F.97, A:A.124, A:A.127, A:T.160, A:Y.162, A:F.167, A:A.176, A:I.177, A:F.180, A:F.180, B:Y.210 Hydrogen bonds: A:S.244 Metal complexes: A:H.173 BCL.2: 22 residues within 4Å: Chain A: I.49, Y.128, L.131, F.146, I.150, W.151, H.153, L.154, V.157 Chain B: F.197, G.203, I.206, A.207, Y.210, G.211, L.214 Ligands: BCL.1, BPH.3, LDA.26, BCL.37, U10.40, LDA.52 13 PLIP interactions: 7 interactions with chain A, 6 interactions with chain B, Hydrophobic interactions: A:I.49, A:Y.128, A:L.131, A:F.146, A:L.154, A:V.157, B:F.197, B:I.206, B:I.206, B:Y.210, B:L.214 pi-Stacking: B:Y.210 Metal complexes: A:H.153 BCL.36: 22 residues within 4Å: Chain A: H.168, M.174, I.177, S.178, F.181, T.182, L.185 Chain B: M.122, W.157, L.160, V.175, I.179, H.182, L.183, T.186 Ligands: BCL.1, U10.4, LDA.31, LDA.33, BCL.37, BPH.38, SPO.41 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B, Hydrophobic interactions: A:I.177, A:I.177, A:L.185, B:L.160, B:V.175, B:I.179, B:L.183 Hydrogen bonds: A:S.178 Metal complexes: B:H.182 pi-Stacking: A:F.181 BCL.37: 31 residues within 4Å: Chain A: V.157, Y.162, H.168, F.181 Chain B: M.122, V.126, 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, I.284 Ligands: BCL.1, BCL.2, U10.4, BCL.36, BPH.38, LDA.57 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:V.126, B:A.153, B:L.156, B:W.157, B:T.186, B:F.189, B:L.196, 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: 32 residues within 4Å: Chain A: T.38, F.41, A.42, I.49, A.93, A.96, F.97, W.100, E.104, I.117, A.120, F.121, F.123, 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, T.255, M.256 Ligands: BCL.1, BCL.2, U10.40 18 PLIP interactions: 16 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:I.49, A:A.96, A:A.120, A:F.121, A:F.121, A:F.123, A:A.124, A:Y.128, A:F.146, A:Y.148, A:L.238, A:V.241, A:V.241, B:Y.210, B:A.213 Hydrogen bonds: A:W.100, A:E.104 pi-Stacking: A:F.121 BPH.38: 26 residues within 4Å: Chain A: F.181, A.184, L.185, L.189, F.216, L.219, V.220 Chain B: S.59, L.60, G.63, L.64, W.66, F.67, A.125, V.126, W.129, T.133, T.146, A.149, F.150, A.153, T.277 Ligands: U10.4, BCL.36, BCL.37, LDA.57 14 PLIP interactions: 2 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:A.184, A:L.189, B:L.60, B:L.64, B:W.66, B:F.67, B:W.129, B:A.149, B:F.150, B:F.150, B:A.153, B:T.277 Hydrogen bonds: B:W.129 pi-Stacking: B:F.150

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

U10.4: 28 residues within 4Å: Chain A: M.174, S.178, F.179, T.182, A.186, L.189, H.190, L.193, V.194, E.212, D.213, F.216, Y.222, S.223, I.224, G.225, T.226, I.229 Chain B: W.66, F.67, L.89, F.90 Ligands: UQ1.5, LDA.33, BCL.36, BCL.37, BPH.38, SPO.41 16 PLIP interactions: 12 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:F.179, A:F.179, A:T.182, A:A.186, A:L.189, A:L.193, A:I.224, A:I.229, A:I.229, B:W.66, B:L.89, B:F.90, B:F.90 Hydrogen bonds: A:H.190, A:I.224, A:G.225 U10.40: 26 residues within 4Å: Chain A: V.26, Y.30, G.35, F.39, W.100, R.103 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.3, LDA.25 17 PLIP interactions: 4 interactions with chain A, 13 interactions with chain B Hydrophobic interactions: A:V.26, A:F.39, A:W.100, A:W.100, B:L.214, B:M.218, B:H.219, B:W.252, B:M.256, B:F.258, B:F.258, B:A.260, B:I.265, B:I.265, B:W.268, B:W.268 Hydrogen bonds: B:A.260

1 x UQ1: UBIQUINONE-1(Non-covalent)

UQ1.5: 9 residues within 4Å: Chain A: W.263, W.265, W.266 Chain B: L.86, R.87, L.89, F.90 Ligands: U10.4, LDA.34 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: B:L.89, B:F.90, B:F.90 pi-Stacking: A:W.266, A:W.266, B:F.90 Hydrogen bonds: B:F.90

7 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.6: 4 residues within 4Å: Chain A: E.72, Y.73, K.82 Ligands: GOL.17 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.72, A:Y.73 Salt bridges: A:K.82 PO4.7: 6 residues within 4Å: Chain A: F.24, W.25, V.26 Chain C: E.94, G.95, F.96 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.25 PO4.8: 6 residues within 4Å: Chain A: Y.162, G.165, N.166 Chain B: N.187, L.191 Ligands: GOL.46 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.166, B:N.187 Water bridges: A:G.165, A:N.166 PO4.9: 4 residues within 4Å: Chain A: M.139, G.140, A.141, Y.144 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.144, A:Y.144 PO4.44: 4 residues within 4Å: Chain B: N.25, N.28, G.53, S.54 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.25, B:S.54, B:S.54 Water bridges: B:N.28, B:Y.51, B:S.54, B:S.54, B:L.55 PO4.45: 6 residues within 4Å: Chain B: E.173, W.185, N.188, F.189, H.193 Ligands: GOL.48 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.173, B:E.173, B:W.185 Water bridges: B:N.188 PO4.59: 5 residues within 4Å: Chain C: K.146, V.198, Q.199, S.200 Ligands: GOL.68 No protein-ligand interaction detected (PLIP)

1 x DIO: 1,4-DIETHYLENE DIOXIDE(Non-covalent)

DIO.10: 6 residues within 4Å: Chain A: I.250, I.254, W.259, W.262 Ligands: GOL.20, LDA.30 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.262

26 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 8 residues within 4Å: Chain A: S.52, L.55, S.65, V.66, Y.67, L.80, A.81, L.85 Ligand excluded by PLIP GOL.12: 5 residues within 4Å: Chain A: A.198, N.199, P.200 Chain C: T.63, F.64 Ligand excluded by PLIP GOL.13: 8 residues within 4Å: Chain A: R.109, G.112, I.113, G.114, Y.115 Chain C: L.241 Chain B: E.2, R.228 Ligand excluded by PLIP GOL.14: 8 residues within 4Å: Chain A: E.205, M.206, R.207, T.208, H.211 Chain C: P.67, G.125 Chain B: E.22 Ligand excluded by PLIP GOL.15: 2 residues within 4Å: Chain A: N.60 Ligands: HT3.23 Ligand excluded by PLIP GOL.16: 3 residues within 4Å: Chain A: D.261, W.265 Ligands: GOL.20 Ligand excluded by PLIP GOL.17: 3 residues within 4Å: Chain A: E.72, Y.73 Ligands: PO4.6 Ligand excluded by PLIP GOL.18: 6 residues within 4Å: Chain A: G.77, A.78, G.84, Q.87, I.88 Ligands: LDA.29 Ligand excluded by PLIP GOL.19: 1 residues within 4Å: Chain A: Y.67 Ligand excluded by PLIP GOL.20: 6 residues within 4Å: Chain A: W.255, W.262, W.265 Ligands: DIO.10, GOL.16, LDA.33 Ligand excluded by PLIP GOL.21: 3 residues within 4Å: Chain A: P.12, N.20 Chain C: T.90 Ligand excluded by PLIP GOL.22: 4 residues within 4Å: Chain A: Y.115, H.116, F.119 Chain B: Q.4 Ligand excluded by PLIP GOL.46: 3 residues within 4Å: Chain A: Y.162 Chain B: L.191 Ligands: PO4.8 Ligand excluded by PLIP GOL.47: 4 residues within 4Å: Chain B: L.18, S.30, G.31, P.49 Ligand excluded by PLIP GOL.48: 4 residues within 4Å: Chain B: S.172, E.173 Ligands: PO4.45, GOL.50 Ligand excluded by PLIP GOL.49: 6 residues within 4Å: Chain B: E.2, Y.3, Q.4, N.5, I.6, F.7 Ligand excluded by PLIP GOL.50: 7 residues within 4Å: Chain B: E.95, P.96, P.97, A.98, P.99, S.172 Ligands: GOL.48 Ligand excluded by PLIP GOL.60: 10 residues within 4Å: Chain C: R.177, F.178, P.192, Q.194, E.230, C.234 Chain B: S.227, R.228, G.230, R.233 Ligand excluded by PLIP GOL.61: 3 residues within 4Å: Chain C: N.44, T.48, P.49 Ligand excluded by PLIP GOL.62: 3 residues within 4Å: Chain A: P.12, G.13 Chain C: M.242 Ligand excluded by PLIP GOL.63: 3 residues within 4Å: Chain C: Q.199, R.202 Ligands: GOL.68 Ligand excluded by PLIP GOL.64: 7 residues within 4Å: Chain C: E.38, T.74, V.75, G.77, P.78, E.79 Chain B: R.241 Ligand excluded by PLIP GOL.65: 4 residues within 4Å: Chain C: I.160, A.161, S.210 Ligands: HTO.69 Ligand excluded by PLIP GOL.66: 3 residues within 4Å: Chain C: H.128, N.129, K.132 Ligand excluded by PLIP GOL.67: 5 residues within 4Å: Chain C: R.154, K.197, Q.199, H.204 Chain B: A.1 Ligand excluded by PLIP GOL.68: 6 residues within 4Å: Chain C: Q.199, S.200, N.201, R.202 Ligands: PO4.59, GOL.63 Ligand excluded by PLIP

1 x HT3: (2R,3S)-HEPTANE-1,2,3-TRIOL(Non-covalent)

HT3.23: 4 residues within 4Å: Chain A: T.58, N.60, L.63 Ligands: GOL.15 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.58, A:N.60 Water bridges: A:W.59

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

HTO.24: 5 residues within 4Å: Chain A: I.46, I.49, W.59, I.64 Ligands: LDA.26 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.59, A:I.64 HTO.69: 7 residues within 4Å: Chain C: I.160, G.162, K.163, E.182, L.183, K.184 Ligands: GOL.65 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:K.184, C:K.184 Hydrogen bonds: C:E.182

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

LDA.25: 6 residues within 4Å: Chain A: P.28 Chain B: M.256, G.257, F.258 Ligands: U10.40, LDA.70 Ligand excluded by PLIP LDA.26: 7 residues within 4Å: Chain A: P.61, I.64, Y.148, G.149 Ligands: BCL.2, HTO.24, LDA.71 Ligand excluded by PLIP LDA.27: 6 residues within 4Å: Chain A: A.101, R.109, Y.115, P.118, F.119 Ligands: LDA.32 Ligand excluded by PLIP LDA.28: 6 residues within 4Å: Chain A: G.77, Q.87, T.90, I.91, L.133, W.142 Ligand excluded by PLIP LDA.29: 4 residues within 4Å: Chain A: L.44, I.88, I.91 Ligands: GOL.18 Ligand excluded by PLIP LDA.30: 3 residues within 4Å: Chain A: I.254 Ligands: DIO.10, LDA.33 Ligand excluded by PLIP LDA.31: 6 residues within 4Å: Chain A: V.220, G.221 Chain B: S.30, G.33 Ligands: BCL.36, LDA.57 Ligand excluded by PLIP LDA.32: 8 residues within 4Å: Chain A: F.119, A.122, F.123, L.126, V.241, F.242, A.245 Ligands: LDA.27 Ligand excluded by PLIP LDA.33: 6 residues within 4Å: Chain A: M.174, W.265 Ligands: U10.4, GOL.20, LDA.30, BCL.36 Ligand excluded by PLIP LDA.34: 2 residues within 4Å: Chain A: W.271 Ligands: UQ1.5 Ligand excluded by PLIP LDA.35: 7 residues within 4Å: Chain A: F.123, L.234, L.235, L.238, S.239, F.242 Chain B: I.6 Ligand excluded by PLIP LDA.52: 12 residues within 4Å: Chain A: W.151 Chain C: L.24, L.31 Chain B: P.200, L.204, A.207, F.208, W.268, M.272 Ligands: BCL.2, LDA.70, LDA.73 Ligand excluded by PLIP LDA.53: 5 residues within 4Å: Chain B: F.7, L.38, L.39, W.41, F.42 Ligand excluded by PLIP LDA.54: 6 residues within 4Å: Chain C: L.12 Chain B: L.167, M.168, L.285, G.288, T.289 Ligand excluded by PLIP LDA.55: 4 residues within 4Å: Chain B: F.105, A.107, G.113, F.120 Ligand excluded by PLIP LDA.56: 5 residues within 4Å: Chain B: W.127, S.128, G.131, Y.134, Q.138 Ligand excluded by PLIP LDA.57: 6 residues within 4Å: Chain A: V.220 Chain B: I.50, W.129 Ligands: LDA.31, BCL.37, BPH.38 Ligand excluded by PLIP LDA.70: 10 residues within 4Å: Chain C: Q.32, Y.40, Q.53, F.56 Chain B: R.253, F.258, W.268 Ligands: LDA.25, LDA.52, LDA.73 Ligand excluded by PLIP LDA.71: 3 residues within 4Å: Chain C: W.21 Ligands: LDA.26, LDA.73 Ligand excluded by PLIP LDA.72: 4 residues within 4Å: Chain C: A.25, I.28, Y.29 Ligands: LDA.73 Ligand excluded by PLIP LDA.73: 8 residues within 4Å: Chain C: Y.18, W.21, A.25, I.28 Ligands: LDA.52, LDA.70, LDA.71, LDA.72 Ligand excluded by PLIP

1 x FE: FE (III) ION(Non-covalent)

FE.39: 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 SPO: SPHEROIDENE(Non-covalent)

SPO.41: 22 residues within 4Å: Chain B: F.67, I.70, G.71, F.74, W.75, F.85, W.115, S.119, F.120, M.122, W.157, L.160, G.161, F.162, W.171, V.175, Y.177, G.178, I.179, H.182 Ligands: U10.4, BCL.36 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:F.67, B:F.67, B:F.67, B:I.70, B:I.70, B:F.74, B:F.85, B:W.115, B:F.120, B:W.157, B:L.160, B:F.162, B:F.162, B:W.171, B:V.175, B:V.175, B:Y.177, B:I.179 Hydrogen bonds: B:W.75

2 x K: POTASSIUM ION(Non-covalent)

K.42: 2 residues within 4Å: Chain B: V.192, D.292 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:V.192, B:D.292 K.58: 3 residues within 4Å: Chain C: M.134, A.137, F.140 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:M.134, C:A.137, C:F.140, H2O.5033, H2O.5033

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

CL.43: 4 residues within 4Å: Chain C: Y.30 Chain B: R.267, W.271 Ligands: CDL.51 Ligand excluded by PLIP

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.51: 18 residues within 4Å: Chain A: N.199, P.200 Chain C: F.20, I.22, F.23, G.26, L.27, Y.30 Chain B: G.143, K.144, H.145, W.148, W.155, R.267, I.270, W.271, L.278 Ligands: CL.43 23 PLIP interactions: 1 interactions with chain A, 5 interactions with chain C, 17 interactions with chain B Hydrogen bonds: A:N.199, B:K.144, B:W.148, B:R.267 Hydrophobic interactions: C:I.22, C:F.23, C:L.27, C:Y.30, B:W.148, B:W.148, B:W.148, B:W.148, B:W.148, B:W.155, B:I.270, B:W.271, B:L.278 Salt bridges: B:H.145, B:H.145, B:H.145, B:R.267 Water bridges: C:K.62, B:K.144

Links

RCSB   PDBe   PDBj   PDBsum   CATH   PLIP

Citation

Fujii, R. et al., Structure of the carotenoid bound to the reaction centre from Rhodobacter sphaeroides 2.4.1 revealed by time-resolved X-ray crystallography. To be Published

Release Date

2010-12-01

Peptides

Reaction center protein L chain: A
Reaction center protein M chain: B
Reaction center protein H chain: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
L

B
M

C
H

Reaction center protein L chain

Reaction center protein M chain

Reaction center protein H chain

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