SMTL ID : 8c7c.1

Double mutant V(M84)C/A(L278)C structure of Photosynthetic Reaction Center From Cereibacter sphaeroides strain RV

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

LDA.1: 8 residues within 4Å: Chain A: Q.23, Y.31, G.45, F.47 Chain C: R.253, F.258 Ligands: LDA.23, LDA.28 7 PLIP interactions: 2 interactions with chain A, 5 interactions with chain C Hydrophobic interactions: A:F.47, C:F.258, C:F.258, C:F.258 Hydrogen bonds: A:Y.31, C:R.253, C:R.253 LDA.9: 7 residues within 4Å: Chain B: V.220, G.221 Chain C: S.30, G.31, V.32, G.33 Ligands: UNL.25 No protein-ligand interaction detected (PLIP) LDA.23: 4 residues within 4Å: Chain C: A.207, M.272 Ligands: LDA.1, BCL.7 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.207 LDA.24: 5 residues within 4Å: Chain C: F.7, T.8, L.38, W.41, F.42 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.7, C:L.38, C:F.42 pi-Cation interactions: C:W.41 LDA.28: 11 residues within 4Å: Chain B: P.28, F.29 Chain C: M.256, G.257, F.258 Ligands: LDA.1, UNL.2, UNL.3, BCL.6, BCL.7, U10.21 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.258, C:F.258

8 x UNL: UNKNOWN LIGAND

UNL.2: 5 residues within 4Å: Chain A: Y.9, W.12, I.13, A.16 Ligands: LDA.28 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.12, A:W.12, A:I.13, A:A.16 UNL.3: 4 residues within 4Å: Chain A: W.12 Ligands: BCL.7, HTO.15, LDA.28 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.12 UNL.10: 8 residues within 4Å: Chain B: L.75, G.76, G.77, Q.87, T.90, I.91, T.94, W.142 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:I.91, B:I.91, B:T.94, B:W.142 UNL.11: 5 residues within 4Å: Chain B: A.101, Y.115, P.118, F.119 Ligands: UNL.27 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:A.101, B:Y.115, B:Y.115, B:P.118 UNL.12: 3 residues within 4Å: Chain B: F.134, F.242, A.245 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.134, B:F.242, B:A.245 UNL.25: 6 residues within 4Å: Chain B: V.220 Chain C: L.52, W.129 Ligands: LDA.9, BCL.18, BPH.19 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:L.52, C:W.129, B:V.220 UNL.26: 5 residues within 4Å: Chain C: L.167, L.285, L.286, G.288, V.290 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.285, C:L.286, C:V.290 UNL.27: 4 residues within 4Å: Chain B: F.119 Chain C: E.2, Q.4 Ligands: UNL.11 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:E.2, C:Q.4, B:F.119, B:F.119, B:F.119

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 9 residues within 4Å: Chain A: R.168, F.169, Q.185, E.221, C.225 Chain C: S.227, R.228, G.230, R.233 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrogen bonds: A:R.168, A:R.168, A:Q.185, C:G.230, C:R.233 EDO.5: 6 residues within 4Å: Chain A: S.71, E.72, D.73, V.106, A.107 Chain C: R.241 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:R.241, A:A.107 EDO.13: 5 residues within 4Å: Chain B: F.123, L.126, V.241, F.242, A.245 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.241 EDO.14: 7 residues within 4Å: Chain A: L.232 Chain B: G.112, I.113, G.114, Y.115 Chain C: E.2, R.228 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:R.228, C:R.228 Water bridges: B:Y.115

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.6: 29 residues within 4Å: Chain B: F.97, A.124, I.125, A.127, 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.210 Ligands: BCL.7, BPH.8, BCL.17, BCL.18, U10.21, LDA.28 15 PLIP interactions: 14 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:F.97, B:F.97, B:A.124, B:V.157, B:T.160, B:Y.162, 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.7: 20 residues within 4Å: Chain B: Y.128, L.131, F.146, I.150, H.153, L.154 Chain C: F.197, G.203, I.206, A.207, Y.210, G.211, L.214 Ligands: UNL.3, BCL.6, BPH.8, BCL.18, U10.21, LDA.23, LDA.28 13 PLIP interactions: 5 interactions with chain B, 8 interactions with chain C, Hydrophobic interactions: B:Y.128, B:L.131, B:F.146, B:L.154, C:F.197, C:I.206, C:I.206, C:A.207, C:Y.210, C:Y.210, C:L.214 Metal complexes: B:H.153 pi-Stacking: C:Y.210 BCL.17: 18 residues within 4Å: Chain B: H.168, M.174, I.177, T.178, F.181, T.182, L.185 Chain C: F.67, W.157, V.175, I.179, H.182, L.183, T.186 Ligands: BCL.6, BCL.18, BPH.19, SPN.22 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain C, Hydrophobic interactions: B:I.177, B:I.177, B:T.182, B:L.185, C:F.67, C:V.175, C:I.179, C:L.183, C:T.186 Hydrogen bonds: B:T.178 Metal complexes: C:H.182 BCL.18: 26 residues within 4Å: Chain B: V.157, Y.162, F.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.6, BCL.7, BCL.17, BPH.19, UNL.25 13 PLIP interactions: 13 interactions with chain C, Hydrophobic interactions: C:A.153, C:L.156, C:W.157, C:W.157, C:T.186, C:F.189, C:L.196, C:F.197, C:F.197, C:I.206, C:L.209, C:V.276 Metal complexes: C:H.202

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.8: 28 residues within 4Å: Chain B: A.42, I.49, A.93, A.96, F.97, W.100, E.104, I.117, A.120, F.121, F.123, A.124, Y.128, Y.148, G.149, I.150, H.153, L.238, V.241 Chain C: Y.210, A.213, L.214, M.218, W.252, M.256 Ligands: BCL.6, BCL.7, U10.21 15 PLIP interactions: 2 interactions with chain C, 13 interactions with chain B Hydrophobic interactions: C:Y.210, C:A.213, B:A.42, B:I.49, B:A.96, B:F.97, B:A.120, B:F.121, B:F.121, B:F.121, B:F.123, B:Y.148, B:L.238, B:V.241, B:V.241 BPH.19: 23 residues within 4Å: Chain B: F.181, A.184, L.185, A.188, L.189, L.219 Chain C: S.59, L.60, G.63, L.64, F.67, A.125, V.126, W.129, T.146, A.149, F.150, A.153, A.273, T.277 Ligands: BCL.17, BCL.18, UNL.25 12 PLIP interactions: 9 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:L.64, C:F.67, C:F.67, C:A.149, C:F.150, C:F.150, C:F.150, C:A.153, C:T.277, B:A.184, B:A.188, B:L.189

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

HTO.15: 6 residues within 4Å: Chain B: I.49, P.61, I.64, Y.148, I.150 Ligands: UNL.3 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:P.61, B:I.64

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.16: 15 residues within 4Å: Chain A: I.13, F.14, G.17, Y.21 Chain B: N.199, P.200, K.202 Chain C: G.143, K.144, H.145, W.148, R.267, W.271, V.274, L.278 15 PLIP interactions: 11 interactions with chain C, 1 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: C:W.148, C:W.148, C:V.274, C:L.278, C:L.278, A:I.13, A:Y.21, A:Y.21 Hydrogen bonds: C:K.144, B:K.202 Water bridges: C:R.267 Salt bridges: C:H.145, C:H.145, C:H.145, C:R.267

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

FE.20: 5 residues within 4Å: Chain B: H.190, H.230 Chain C: H.219, E.234, H.266 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain C Metal complexes: B:H.190, B:H.230, C:H.219, C:E.234, C:H.266

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

U10.21: 27 residues within 4Å: Chain B: F.29, Y.30, V.31, G.35, T.38, W.100 Chain C: 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.6, BCL.7, BPH.8, LDA.28 18 PLIP interactions: 13 interactions with chain C, 5 interactions with chain B Hydrophobic interactions: C:L.214, C:M.218, C:W.252, C:M.256, C:F.258, C:F.258, C:A.260, C:I.265, C:I.265, C:W.268, C:W.268, B:F.29, B:F.29, B:V.31, B:T.38, B:W.100 Hydrogen bonds: C:T.222, C:A.260

1 x SPN: SPEROIDENONE(Non-covalent)

SPN.22: 23 residues within 4Å: Chain C: F.67, F.68, I.70, G.71, F.74, W.75, L.89, F.105, S.119, F.120, M.122, F.123, W.157, G.161, F.162, W.171, V.175, P.176, Y.177, G.178, I.179, H.182 Ligands: BCL.17 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:F.67, C:F.67, C:F.67, C:F.68, C:I.70, C:F.74, C:F.74, C:L.89, C:F.105, C:F.120, C:F.123, C:W.157, C:F.162, C:F.162, C:W.171, C:V.175, C:V.175, C:Y.177, C:Y.177, C:I.179

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Selikhanov, G. et al., Stabilization of Cereibacter sphaeroides Photosynthetic Reaction Center by the Introduction of Disulfide Bonds. Membranes (Basel) (2023)

Release Date

2023-11-22

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.
Show / Hide

Reaction center protein H chain

Reaction center protein L chain

Reaction center protein M chain

Related Entries With Identical Sequence