SMTL ID : 1ds8.2 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-oligomer

Ligands

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

FE2.1: 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 CD: CADMIUM ION(Non-covalent)

CD.2: 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.171, H2O.210

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

CL.3: 4 residues within 4Å: Chain A: N.199 Chain B: H.145, R.267 Ligands: LDA.13 Ligand excluded by PLIP

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.4: 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.5, BCL.6, BPH.8, LDA.12 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A, Hydrophobic interactions: B:L.160, B:L.183, A:I.177, A:I.177, A:L.185 Metal complexes: B:H.182 Hydrogen bonds: A:T.182 pi-Stacking: A:F.181 BCL.5: 29 residues within 4Å: Chain A: F.97, F.121, 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, C.247, M.248 Chain B: Y.210 Ligands: BCL.4, BCL.6, BCL.7, BPH.9, 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:F.121, 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.6: 26 residues within 4Å: Chain A: V.157, Y.162, F.181 Chain B: 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, G.280, I.284 Ligands: BCL.4, BCL.5, BCL.7, BPH.8 15 PLIP interactions: 13 interactions with chain B, 2 interactions with chain A, Hydrophobic interactions: B:V.126, 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 Metal complexes: B:H.202 BCL.7: 19 residues within 4Å: Chain A: I.46, Y.128, L.131, F.146, H.153, L.154, V.157 Chain B: F.197, G.203, I.206, A.207, Y.210, G.211, L.214 Ligands: BCL.5, BCL.6, BPH.9, U10.10, LDA.14 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B, Hydrophobic interactions: A:I.46, A:L.131, 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

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.8: 22 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.4, BCL.6 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:W.129, B:W.129, B:A.149, B:F.150, B:F.150, B:F.150, B:A.273, B:T.277, A:A.184, A:A.188, A:L.189 pi-Stacking: B:F.150 BPH.9: 32 residues within 4Å: Chain A: T.38, F.41, A.42, G.45, I.46, I.49, A.96, F.97, W.100, E.104, I.117, A.120, F.121, A.124, F.146, Y.148, G.149, I.150, H.153, S.237, L.238, V.241 Chain B: Y.210, A.213, L.214, M.218, W.252, T.255, M.256 Ligands: BCL.5, BCL.7, U10.10 15 PLIP interactions: 12 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:A.42, A:I.49, A:A.120, A:F.121, A:F.121, A:A.124, A:F.146, A:Y.148, A:Y.148, A:L.238, A:V.241, A:V.241, B:Y.210, B:A.213, B:L.214

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

U10.10: 19 residues within 4Å: Chain A: W.100 Chain B: 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: BCL.5, BCL.7, BPH.9 13 PLIP interactions: 12 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:M.218, B:H.219, B:W.252, B:M.256, B:F.258, B:A.260, B:I.265, B:I.265, B:W.268, B:W.268, A:W.100 Hydrogen bonds: B:T.222, B:A.260 U10.11: 12 residues within 4Å: Chain A: T.182, A.186, L.189, H.190, L.193, F.216, Y.222, S.223, I.224, G.225, I.229, L.232 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:T.182, A:L.232 Hydrogen bonds: A:I.224 pi-Stacking: A:F.216

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

LDA.12: 10 residues within 4Å: Chain B: F.67, I.70, G.71, F.74, F.85, V.175, P.176, Y.177, G.178 Ligands: BCL.4 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.67, B:I.70, B:V.175, B:Y.177 LDA.13: 8 residues within 4Å: Chain B: H.145, W.148, L.151, S.152, W.155, W.271, L.278 Ligands: CL.3 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.148, B:L.151, B:W.155, B:W.271 Water bridges: B:R.267 LDA.14: 5 residues within 4Å: Chain B: P.200, F.208, M.272 Chain C: W.21 Ligands: BCL.7 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: C:W.21, B:F.208 Water bridges: B:G.203

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
R

B
S

C
T

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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