SMTL ID : 1ds8.1 (1 other biounit)

PHOTOSYNTHETIC REACTION CENTER FROM RHODOBACTER SPHAEROIDES IN THE CHARGE-NEUTRAL DQAQB STATE WITH THE PROTON TRANSFER INHIBITOR CD2+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-1-1-1-mer

Ligands

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 17 residues within 4Å: Chain A: H.168, M.174, I.177, S.178, F.181, T.182, L.185 Chain B: W.157, L.160, I.179, H.182, L.183, T.186 Ligands: BCL.2, BCL.8, BPH.9, LDA.13 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B, Hydrophobic interactions: A:I.177, A:I.177, A:L.185, B:L.160, B:L.183 Water bridges: A:S.178 pi-Stacking: A:F.181 Metal complexes: B:H.182 BCL.2: 29 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.1, BCL.3, BPH.4, BCL.8, U10.10 15 PLIP interactions: 14 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:F.97, A:F.97, A:F.97, 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 pi-Cation interactions: A:H.173 Metal complexes: A:H.173 BCL.3: 19 residues within 4Å: Chain A: Y.128, L.131, F.146, I.150, H.153, L.154, V.157 Chain B: F.197, G.203, I.206, A.207, Y.210, G.211, L.214 Ligands: BCL.2, BPH.4, BCL.8, U10.10, LDA.12 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B, Hydrophobic interactions: A:L.131, A:F.146, A:L.154, A:V.157, B:F.197, B:I.206, B:I.206, B:L.214 Metal complexes: A:H.153 pi-Stacking: B:Y.210 BCL.8: 27 residues within 4Å: Chain A: V.157, Y.162, H.168, F.181 Chain B: W.66, 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.1, BCL.2, BCL.3, BPH.9 17 PLIP interactions: 14 interactions with chain B, 3 interactions with chain A, Hydrophobic interactions: B:W.66, B:L.156, B:W.157, B:T.186, B:F.189, B:L.196, B:F.197, B:I.206, B:L.209, B:Y.210, B:V.276, B:I.284, A:V.157, A:F.181 Hydrogen bonds: B:S.205 Metal complexes: B:H.202 pi-Cation interactions: A:H.168

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.4: 29 residues within 4Å: Chain A: T.38, A.42, I.89, 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, I.150, H.153, V.241 Chain B: Y.210, A.213, L.214, A.217, M.218, W.252, M.256 Ligands: BCL.2, BCL.3, U10.10 19 PLIP interactions: 15 interactions with chain A, 4 interactions with chain B Hydrophobic interactions: A:A.42, A:I.89, 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:Y.148, A:V.241, A:V.241, B:Y.210, B:A.213, B:L.214, B:A.217 Hydrogen bonds: A:E.104 BPH.9: 23 residues within 4Å: Chain A: F.181, A.184, L.185, A.188, L.189, L.219 Chain B: S.59, L.60, G.63, A.125, V.126, W.129, T.133, T.146, A.149, F.150, A.153, A.273, V.274, T.277 Ligands: BCL.1, U10.5, BCL.8 9 PLIP interactions: 3 interactions with chain A, 6 interactions with chain B Hydrophobic interactions: A:A.184, A:A.188, A:L.189, B:W.129, B:A.149, B:F.150, B:F.150, B:F.150 pi-Stacking: B:F.150

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

U10.5: 19 residues within 4Å: Chain A: A.186, L.189, L.193, F.216, V.220, G.221, Y.222, S.223, I.224, G.225, I.229, L.232 Chain B: S.30, G.31, V.32, G.33, G.48, I.50 Ligands: BPH.9 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:V.220, A:Y.222, A:L.232, B:I.50 Hydrogen bonds: A:I.224 pi-Stacking: A:F.216 U10.10: 21 residues within 4Å: Chain A: F.29 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.4 15 PLIP interactions: 14 interactions with chain B, 1 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:I.265, B:W.268, B:W.268, B:W.268, A:F.29 Hydrogen bonds: B:T.222, B:A.260

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

FE2.6: 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.7: 4 residues within 4Å: Chain A: N.199 Chain B: H.145, R.267 Ligands: LDA.11 Ligand excluded by PLIP

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

LDA.11: 8 residues within 4Å: Chain B: H.145, W.148, S.152, I.270, W.271, V.274, L.278 Ligands: CL.7 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:W.271, B:W.271, B:V.274, B:L.278 LDA.12: 7 residues within 4Å: Chain B: P.200, G.203, L.204, F.208, M.272 Chain C: W.21 Ligands: BCL.3 No protein-ligand interaction detected (PLIP) LDA.13: 12 residues within 4Å: Chain B: F.67, W.115, M.122, L.160, G.161, A.174, V.175, Y.177, G.178, I.179, H.182 Ligands: BCL.1 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.67, B:V.175, B:Y.177, B:I.179 Hydrogen bonds: B:V.175

1 x CD: CADMIUM ION(Non-covalent)

CD.14: 3 residues within 4Å: Chain C: D.124, H.126, H.128 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.124, C:H.126, C:H.128, H2O.10, H2O.10

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Axelrod, H.L. et al., Determination of the binding sites of the proton transfer inhibitors Cd2+ and Zn2+ in bacterial reaction centers. Proc.Natl.Acad.Sci.USA (2000)

Release Date

2000-03-08

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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