SMTL ID : 1rzh.1

PHOTOSYNTHETIC REACTION CENTER DOUBLE MUTANT FROM RHODOBACTER SPHAEROIDES WITH ASP L213 REPLACED WITH ASN AND ARG M233 REPLACED WITH CYS IN THE CHARGE-NEUTRAL DQAQB STATE (TRIGONAL FORM)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-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, S.244, C.247, M.248 Chain B: T.186, Y.210 Ligands: BCL.2, BPH.3, BCL.9, BCL.10, U10.12 16 PLIP interactions: 15 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:F.97, A:F.97, A:F.97, A:F.97, A:A.124, A:Y.128, 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.46, 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, BCL.10, U10.12, LDA.14 13 PLIP interactions: 7 interactions with chain A, 6 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:I.206, B:Y.210, B:L.214 Metal complexes: A:H.153 pi-Stacking: B:Y.210 BCL.9: 18 residues within 4Å: Chain A: H.168, M.174, I.177, S.178, 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, BCL.10, BPH.11, SPO.13 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A, Hydrophobic interactions: B:L.160, B:V.175, B:L.183, A:I.177, A:L.185 Metal complexes: B:H.182 Hydrogen bonds: A:T.182 BCL.10: 28 residues within 4Å: Chain A: V.157, Y.162, F.181 Chain B: W.66, 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, Y.210, V.276, T.277, G.280, I.284 Ligands: BCL.1, BCL.2, BCL.9, BPH.11 13 PLIP interactions: 13 interactions with chain B, Hydrophobic interactions: B:W.66, B:V.126, B:A.153, B:L.156, B:W.157, B:W.157, B:T.186, B:F.189, B:L.196, B:I.206, 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, I.89, A.93, A.96, F.97, W.100, E.104, I.117, A.120, F.121, F.123, A.124, Y.148, G.149, I.150, H.153, L.238, V.241 Chain B: Y.210, A.213, L.214, A.217, M.218, W.252, T.255, M.256 Ligands: BCL.1, BCL.2, U10.12 20 PLIP interactions: 4 interactions with chain B, 16 interactions with chain A Hydrophobic interactions: B:Y.210, B:A.213, B:L.214, B:A.217, A:A.42, A:I.49, A:I.89, A:A.93, A:A.96, A:A.120, A:F.121, A:F.121, A:F.123, A:A.124, A:Y.148, A:Y.148, A:Y.148, A:L.238, A:V.241 pi-Stacking: A:F.121 BPH.11: 25 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, F.67, A.125, V.126, W.129, T.133, T.146, A.149, F.150, A.153, A.273, V.274, T.277 Ligands: U10.4, BCL.9, BCL.10 13 PLIP interactions: 10 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.60, B:L.64, B:F.67, B:A.125, B:W.129, B:A.149, B:F.150, B:F.150, B:T.277, A:A.184, A:L.185, A:L.189 pi-Stacking: B:F.150

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

U10.4: 15 residues within 4Å: Chain A: T.182, A.186, L.189, H.190, L.193, F.216, V.220, Y.222, S.223, I.224, I.229, L.232 Chain B: I.50, W.129 Ligands: BPH.11 7 PLIP interactions: 5 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.182, A:L.189, A:V.220, A:L.232, B:I.50, B:W.129 Hydrogen bonds: A:I.224 U10.12: 30 residues within 4Å: Chain A: F.29, Y.30, V.31, G.35, T.38, 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.1, BCL.2, BPH.3, HTO.6, LDA.18 20 PLIP interactions: 12 interactions with chain B, 8 interactions with chain A 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, A:F.29, A:F.29, A:V.31, A:T.38, A:F.39, A:W.100, A:W.100, A:W.100 Hydrogen bonds: B:T.222, B:A.260

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

HTO.5: 5 residues within 4Å: Chain A: A.101, V.105, P.118, F.119, A.122 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.101, A:A.122 HTO.6: 5 residues within 4Å: Chain A: F.29 Chain B: G.257, F.258 Ligands: U10.12, LDA.18 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.258, B:F.258

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

FE2.7: 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 PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 3 residues within 4Å: Chain B: N.28, G.53, S.54 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.28, B:S.54, B:S.54 Water bridges: B:N.25

1 x SPO: SPHEROIDENE(Non-covalent)

SPO.13: 23 residues within 4Å: Chain B: F.67, F.68, I.70, G.71, W.75, F.85, L.89, S.119, F.120, M.122, F.123, W.157, M.158, L.160, G.161, F.162, W.171, V.175, Y.177, G.178, I.179, H.182 Ligands: BCL.9 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:F.67, B:F.67, B:F.68, B:I.70, B:I.70, B:F.85, B:L.89, B:F.120, B:F.123, B:W.157, B:L.160, B:F.162, B:W.171, B:V.175, B:V.175, B:I.179, B:H.182

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

LDA.14: 10 residues within 4Å: Chain B: P.200, G.203, L.204, A.207, F.208, W.268 Chain C: W.21, L.31 Ligands: BCL.2, LDA.18 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.204, B:A.207, B:F.208, B:W.268, C:L.31 Hydrogen bonds: B:P.200 Water bridges: B:G.203 LDA.15: 5 residues within 4Å: Chain B: F.7, L.38, L.39, W.41, F.42 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.7, B:F.7, B:L.38, B:F.42 pi-Cation interactions: B:F.7, B:W.41, B:W.41 LDA.18: 11 residues within 4Å: Chain B: R.253, W.268 Chain C: I.28, Q.32, Y.40, Q.53, G.54, F.56 Ligands: HTO.6, U10.12, LDA.14 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:I.28, C:F.56, B:W.268 Hydrogen bonds: C:Y.40 Water bridges: C:Q.32

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.16: 9 residues within 4Å: Chain A: N.199, P.200 Chain B: G.143, K.144, H.145, W.148, R.267, W.271 Chain C: Y.30 14 PLIP interactions: 1 interactions with chain A, 10 interactions with chain B, 3 interactions with chain C Water bridges: A:N.199, B:K.144, B:R.267, C:Y.30, C:K.62 Hydrophobic interactions: B:W.148, B:W.148, B:W.148, B:W.271, C:Y.30 Hydrogen bonds: B:K.144 Salt bridges: B:H.145, B:H.145, B:R.267

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.17: 5 residues within 4Å: Chain A: W.263, W.266 Chain B: L.86, L.89, F.90 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Water bridges: B:L.86, A:W.266

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, Q. et al., X-Ray Structure Determination of Three Mutants of the Bacterial Photosynthetic Reaction Centers from Rb. sphaeroides; Altered Proton Transfer Pathways. STRUCTURE (2004)

Release Date

2004-04-13

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

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

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