SMTL ID : 2wx5.1

Hexa-coordination of a bacteriochlorophyll cofactor in the Rhodobacter sphaeroides reaction centre

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.63 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

LDA.1: 2 residues within 4Å: Chain A: W.21 Ligands: LDA.15 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.21, A:W.21, A:W.21 pi-Cation interactions: A:W.21 LDA.13: 9 residues within 4Å: Chain C: P.200, L.204, A.207, F.208, W.268, M.272, L.275 Ligands: BCL.11, LDA.14 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:A.207, C:F.208, C:W.268, C:L.275 LDA.14: 10 residues within 4Å: Chain A: Q.32, Y.40, G.54, F.56 Chain C: R.253, G.257, F.258 Ligands: LDA.13, LDA.15, U10.23 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:F.56, C:F.258, C:F.258, C:F.258 Hydrogen bonds: A:Y.40 LDA.15: 8 residues within 4Å: Chain B: P.28, F.29 Chain C: M.256, G.257 Ligands: LDA.1, BCL.11, LDA.14, U10.23 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:P.28, B:F.29 LDA.16: 6 residues within 4Å: Chain B: V.220, G.221 Chain C: G.31, V.32, G.33 Ligands: HTO.8 No protein-ligand interaction detected (PLIP) LDA.17: 5 residues within 4Å: Chain C: F.7, L.39, W.41, F.42 Ligands: HTO.8 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:F.7, C:L.39, C:W.41, C:F.42 pi-Cation interactions: C:W.41

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

NA.2: 4 residues within 4Å: Chain A: M.134, A.137, G.139, F.140 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.139, A:F.140, A:F.140 NA.18: 2 residues within 4Å: Chain C: N.28, S.54 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:N.28, C:S.54, C:S.54

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.3: 19 residues within 4Å: Chain B: H.168, M.174, I.177, S.178, R.181, T.182 Chain C: F.67, L.89, M.122, W.157, L.160, I.179, H.182, L.183, T.186 Ligands: BCL.4, BCL.10, BPH.21, SPN.22 10 PLIP interactions: 5 interactions with chain C, 4 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: C:F.67, C:L.89, C:L.160, C:L.183, B:I.177, B:I.177 Metal complexes: C:H.182, H2O.8 Hydrogen bonds: B:T.182 pi-Cation interactions: B:R.181 BCL.4: 28 residues within 4Å: Chain B: F.97, A.124, I.125, A.127, Y.128, L.131, W.156, V.157, S.158, G.161, Y.162, N.166, F.167, H.168, H.173, A.176, I.177, F.180, R.181, S.244, A.245, C.247, M.248 Chain C: Y.210 Ligands: BCL.3, BPH.9, BCL.10, BCL.11 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:F.97, B:F.97, B:F.97, B:V.157, B:Y.162, B:F.167, B:F.167, B:A.176, B:I.177, B:I.177, B:F.180, B:F.180, C:Y.210 Hydrogen bonds: B:S.244 Metal complexes: B:H.173 BCL.10: 25 residues within 4Å: Chain B: V.157, Y.162, R.181 Chain C: 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, G.280, I.284 Ligands: BCL.3, BCL.4, BCL.11, BPH.21 15 PLIP interactions: 13 interactions with chain C, 2 interactions with chain B, Hydrophobic interactions: C:L.156, C:W.157, C:T.186, C:F.189, C:L.196, C:F.197, C:I.206, C:L.209, C:Y.210, C:V.276, C:I.284, B:V.157 Hydrogen bonds: C:S.205 Metal complexes: C:H.202 Salt bridges: B:R.181 BCL.11: 19 residues within 4Å: Chain B: Y.128, L.131, F.146, I.150, H.153, L.154, V.157 Chain C: F.197, G.203, I.206, A.207, Y.210, G.211, L.214 Ligands: BCL.4, BPH.9, BCL.10, LDA.13, LDA.15 12 PLIP interactions: 6 interactions with chain C, 6 interactions with chain B, Hydrophobic interactions: C:F.197, C:I.206, C:I.206, C:Y.210, C:L.214, B:Y.128, B:L.131, B:F.146, B:F.146, B:L.154 pi-Stacking: C:Y.210 Metal complexes: B:H.153

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 4 residues within 4Å: Chain A: E.43, E.45, G.47 Chain B: R.7 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:D.46, B:S.4 Hydrogen bonds: B:R.7 GOL.6: 2 residues within 4Å: Chain B: W.262, W.265 No protein-ligand interaction detected (PLIP)

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

HTO.7: 7 residues within 4Å: Chain B: H.190, L.193, F.216, S.223, I.224, G.225, I.229 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.216, B:I.224 Hydrogen bonds: B:H.190, B:I.224, B:G.225 HTO.8: 4 residues within 4Å: Chain B: V.220, Y.222 Ligands: LDA.16, LDA.17 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:Y.222 HTO.20: 8 residues within 4Å: Chain B: W.263, W.265, W.266 Chain C: L.86, R.87, L.89, F.90, F.91 6 PLIP interactions: 5 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:L.89, C:F.90, C:F.90, C:F.90, C:F.91, B:W.266

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.9: 27 residues within 4Å: Chain B: A.42, C.92, A.93, A.96, F.97, W.100, E.104, I.117, A.120, F.121, F.123, A.124, Y.148, I.150, H.153, L.238, V.241 Chain C: Y.210, A.213, L.214, M.218, W.252, T.255, M.256 Ligands: BCL.4, BCL.11, U10.23 16 PLIP interactions: 3 interactions with chain C, 13 interactions with chain B Hydrophobic interactions: C:Y.210, C:A.213, C:L.214, B:A.42, B:A.93, B:F.97, B:A.120, B:F.121, B:F.121, B:F.121, B:F.123, B:A.124, B:Y.148, B:L.238, B:V.241, B:V.241 BPH.21: 22 residues within 4Å: Chain B: R.181, A.184, L.185, L.189, L.219, V.220 Chain C: S.59, L.60, G.63, L.64, F.67, A.125, V.126, W.129, T.133, T.146, A.149, F.150, A.153, T.277 Ligands: BCL.3, BCL.10 15 PLIP interactions: 11 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:L.64, C:F.67, C:F.67, C:W.129, C:W.129, C:A.149, C:F.150, C:F.150, C:A.153, C:T.277, B:R.181, B:A.184, B:L.185, B:L.189 pi-Stacking: C:F.150

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.12: 18 residues within 4Å: Chain A: A.16, I.22, F.23, G.26, L.27, Y.30 Chain B: N.199, P.200, K.202 Chain C: G.143, K.144, H.145, W.148, L.151, R.267, I.270, W.271, L.278 23 PLIP interactions: 15 interactions with chain C, 7 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: C:W.148, C:W.148, C:L.151, C:L.151, C:I.270, C:W.271, C:L.278, A:I.22, A:F.23, A:F.23, A:L.27, A:Y.30, A:Y.30 Hydrogen bonds: C:K.144, B:P.200 Water bridges: C:K.144, C:R.267, A:Y.30 Salt bridges: C:K.144, C:H.145, C:H.145, C:H.145, C:R.267

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

FE.19: 5 residues within 4Å: Chain B: H.190, H.230 Chain C: H.219, E.234, H.266 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Metal complexes: C:H.219, C:E.234, C:H.266, B:H.190, B:H.230

1 x SPN: SPEROIDENONE(Non-covalent)

SPN.22: 22 residues within 4Å: Chain C: F.67, F.68, I.70, G.71, F.74, W.75, F.105, 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: BCL.3 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:F.67, C:F.67, C:F.68, C:I.70, C:F.74, C:F.105, C:W.115, C:W.157, C:L.160, C:F.162, C:W.171, C:V.175, C:Y.177, C:Y.177, C:Y.177, C:I.179

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

U10.23: 23 residues within 4Å: Chain B: F.29, Y.30, G.35, W.100, R.103 Chain C: 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: BPH.9, LDA.14, LDA.15 14 PLIP interactions: 10 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:M.218, C:W.252, C:F.258, C:F.258, C:A.260, C:I.265, C:W.268, C:W.268, B:F.29, B:F.29, B:W.100, B:W.100 Hydrogen bonds: C:T.222, C:A.260

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Frolov, D. et al., Structural and Spectroscopic Consequences of Hexa-Coordination of a Bacteriochlorophyll Cofactor in the Rhodobacter Sphaeroides Reaction Centre. Biochemistry (2010)

Release Date

2010-02-09

Peptides

REACTION CENTER PROTEIN H CHAIN: A
REACTION CENTRE PROTEIN L CHAIN: B
REACTION CENTRE PROTEIN M CHAIN: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

B
L

C
M

Membrane

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

REACTION CENTRE PROTEIN L CHAIN

REACTION CENTRE PROTEIN M CHAIN

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