SMTL ID : 2jiy.1

PHOTOSYNTHETIC REACTION CENTER MUTANT WITH ALA M149 REPLACED WITH TRP (CHAIN M, AM149W)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-oligomer

Ligands

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

LDA.1: 8 residues within 4Å: Chain A: Q.32, Y.40, L.42, G.54, F.56 Chain C: F.259 Ligands: LDA.9, U10.13 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: A:F.56, C:F.259, C:F.259, C:F.259 LDA.9: 11 residues within 4Å: Chain A: W.21 Chain B: W.151 Chain C: P.201, G.204, L.205, A.208, F.209, W.269, M.273 Ligands: LDA.1, BCL.4 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:A.208, C:W.269, A:W.21 Water bridges: C:N.200, C:G.204

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.2: 21 residues within 4Å: Chain B: H.168, P.171, M.174, I.177, S.178, F.179, F.181, T.182, W.263 Chain C: F.91, M.123, W.158, L.161, V.176, I.180, H.183, L.184, T.187 Ligands: BCL.3, BCL.7, SPN.12 13 PLIP interactions: 6 interactions with chain C, 7 interactions with chain B, Hydrophobic interactions: C:F.91, C:L.161, C:V.176, C:I.180, C:L.184, B:P.171, B:M.174, B:I.177, B:I.177, B:F.179, B:W.263 Metal complexes: C:H.183 pi-Stacking: B:F.181 BCL.3: 29 residues within 4Å: Chain B: 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 C: Y.211 Ligands: BCL.2, BCL.4, BPH.5, BCL.7, U10.13 14 PLIP interactions: 13 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:F.97, B:A.124, B:T.160, 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.211 Hydrogen bonds: B:S.244 Metal complexes: B:H.173 BCL.4: 21 residues within 4Å: Chain B: I.46, Y.128, L.131, F.146, I.150, W.151, H.153, L.154, V.157 Chain C: F.198, G.204, I.207, A.208, Y.211, G.212, L.215 Ligands: BCL.3, BPH.5, BCL.7, LDA.9, U10.13 13 PLIP interactions: 7 interactions with chain B, 6 interactions with chain C, Hydrophobic interactions: B:I.46, B:Y.128, B:L.131, B:F.146, B:L.154, B:V.157, C:F.198, C:I.207, C:I.207, C:Y.211, C:L.215 Metal complexes: B:H.153 pi-Stacking: C:Y.211 BCL.7: 24 residues within 4Å: Chain B: V.157, Y.162, F.181 Chain C: W.67, L.157, L.161, T.187, N.188, F.190, S.191, L.197, F.198, H.203, S.206, I.207, L.210, Y.211, V.277, G.281, I.285 Ligands: BCL.2, BCL.3, BCL.4, SPN.12 13 PLIP interactions: 11 interactions with chain C, 2 interactions with chain B, Hydrophobic interactions: C:W.67, C:T.187, C:F.190, C:L.197, C:I.207, C:L.210, C:Y.211, C:V.277, C:I.285, B:F.181, B:F.181 Hydrogen bonds: C:S.206 Metal complexes: C:H.203

1 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.5: 33 residues within 4Å: Chain B: T.38, F.41, A.42, G.45, 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 C: Y.211, A.214, L.215, A.218, M.219, W.253, M.257 Ligands: BCL.3, BCL.4, U10.13 21 PLIP interactions: 17 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:A.42, B:I.49, B:A.96, B:A.120, B:F.121, B:F.121, B:F.121, B:F.123, B:A.124, B:Y.128, B:F.146, B:Y.148, B:Y.148, B:L.238, B:V.241, B:V.241, C:Y.211, C:A.214, C:L.215, C:A.218 Hydrogen bonds: B:E.104

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

U10.6: 17 residues within 4Å: Chain B: T.182, L.185, 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, L.232 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:L.185, B:A.186, B:L.189, B:L.193, B:F.216, B:F.216, B:I.224, B:I.229, B:I.229, B:L.232 Hydrogen bonds: B:I.224, B:G.225 Water bridges: B:T.226 U10.13: 27 residues within 4Å: Chain B: F.29, Y.30, G.35, W.100, R.103 Chain C: M.219, H.220, T.223, I.224, A.246, A.249, A.250, W.253, M.257, F.259, N.260, A.261, T.262, M.263, I.266, W.269, M.273 Ligands: LDA.1, BCL.3, BCL.4, BPH.5, D12.15 17 PLIP interactions: 11 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:M.219, C:W.253, C:M.257, C:F.259, C:F.259, C:A.261, C:I.266, C:I.266, C:W.269, C:W.269, B:F.29, B:F.29, B:F.29, B:W.100, B:W.100, B:W.100 Hydrogen bonds: C:A.261

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.8: 20 residues within 4Å: Chain A: A.16, F.20, I.22, F.23, G.26, L.27, Y.30 Chain B: N.199, P.200 Chain C: G.144, K.145, H.146, W.149, S.153, W.156, R.268, I.271, W.272, V.275, L.279 23 PLIP interactions: 6 interactions with chain A, 15 interactions with chain C, 2 interactions with chain B Hydrophobic interactions: A:F.23, A:F.23, A:L.27, A:Y.30, A:Y.30, C:W.149, C:W.149, C:W.156, C:W.156, C:I.271, C:V.275, C:L.279, C:L.279 Water bridges: A:Y.30, C:K.145, C:R.268 Hydrogen bonds: C:K.145, B:N.199, B:P.200 Salt bridges: C:H.146, C:H.146, C:H.146, C:R.268

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

FE.10: 5 residues within 4Å: Chain B: H.190, H.230 Chain C: H.220, E.235, H.267 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain B Metal complexes: C:H.220, C:E.235, C:H.267, B:H.190, B:H.230

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

PO4.11: 3 residues within 4Å: Chain C: N.29, G.54, S.55 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:N.29, C:S.55 Water bridges: C:N.26, C:Y.52, C:Y.52, C:Y.52

1 x SPN: SPEROIDENONE(Non-covalent)

SPN.12: 24 residues within 4Å: Chain C: W.67, F.68, F.69, I.71, G.72, F.75, W.76, W.116, S.120, F.121, M.123, W.158, M.159, L.161, G.162, F.163, W.172, V.176, Y.178, G.179, I.180, H.183 Ligands: BCL.2, BCL.7 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:W.67, C:F.68, C:I.71, C:I.71, C:F.75, C:W.116, C:F.121, C:W.158, C:L.161, C:F.163, C:F.163, C:W.172, C:V.176, C:Y.178, C:I.180

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

CL.14: 1 residues within 4Å: Chain C: W.130 Ligand excluded by PLIP

1 x D12: DODECANE(Non-covalent)

D12.15: 4 residues within 4Å: Chain C: M.257, G.258, F.259 Ligands: U10.13 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.259

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fyfe, P.K. et al., Structural Responses to Cavity-Creating Mutations in an Integral Membrane Protein. Biochemistry (2007)

Release Date

2007-09-04

Peptides

REACTION CENTER PROTEIN H CHAIN: A
REACTION CENTER PROTEIN L CHAIN: B
REACTION CENTER 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 CENTER PROTEIN L CHAIN

REACTION CENTER PROTEIN M CHAIN

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