SMTL ID : 1ry5.1

PHOTOSYNTHETIC REACTION CENTER MUTANT FROM RHODOBACTER SPHAEROIDES WITH ASP L213 REPLACED WITH ASN

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-1-1-1-mer

Ligands

4 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.1: 19 residues within 4Å: Chain A: H.168, M.174, I.177, S.178, F.181, T.182, L.185 Chain B: M.122, L.156, W.157, L.160, I.179, H.182, L.183, T.186 Ligands: BCL.2, BCL.10, BPH.11, SPO.13 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A, Hydrophobic interactions: B:L.156, 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.2: 28 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.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: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.3: 21 residues within 4Å: Chain A: I.46, I.49, 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.10, U10.12, LDA.15 12 PLIP interactions: 7 interactions with chain A, 5 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:L.214 Metal complexes: A:H.153 pi-Stacking: B:Y.210 BCL.10: 28 residues within 4Å: Chain A: V.157, Y.162, F.181 Chain B: 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, L.209, Y.210, V.276, T.277, G.280, I.284 Ligands: BCL.1, BCL.2, BCL.3, BPH.11 12 PLIP interactions: 12 interactions with chain B, Hydrophobic interactions: B:V.126, B:L.156, B:T.186, B:F.189, B:L.196, B:I.206, B:L.209, B:L.209, B:Y.210, B:V.276, B:T.277 Metal complexes: B:H.202

2 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)

BPH.4: 34 residues within 4Å: Chain A: T.38, F.41, A.42, I.89, C.92, 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, S.237, L.238, V.241 Chain B: Y.210, A.213, L.214, A.217, M.218, W.252, T.255, M.256 Ligands: BCL.2, BCL.3, U10.12 18 PLIP interactions: 14 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.121, A:F.123, A:A.124, A:Y.148, A:Y.148, A:L.238, A:V.241, A:V.241, B:Y.210, B:A.213, B:L.214, B:A.217 BPH.11: 22 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, 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, BCL.10 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:L.60, 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)

U10.5: 14 residues within 4Å: Chain A: T.182, L.189, H.190, L.193, V.194, E.212, N.213, F.216, Y.222, S.223, I.224, G.225, T.226, I.229 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:T.182, A:L.189, A:L.193, A:Y.222, A:I.224, A:I.229, A:I.229 Hydrogen bonds: A:N.213, A:I.224, A:G.225 U10.12: 27 residues within 4Å: Chain A: F.29, Y.30, 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.3, BPH.4, LDA.18 18 PLIP interactions: 5 interactions with chain A, 13 interactions with chain B Hydrophobic interactions: A:F.29, A:F.29, A:T.38, A:W.100, A:W.100, 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 Hydrogen bonds: B:T.222, B:A.260

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: S.4, R.7 Chain C: E.43, G.47, E.81 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain A Hydrogen bonds: C:E.43, A:R.7 Water bridges: C:E.43, C:E.43, C:E.81, C:E.81, A:R.7

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

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

PO4.8: 2 residues within 4Å: Chain B: T.21 Chain C: H.126 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:T.21, B:T.21 Water bridges: B:T.21 Salt bridges: C:H.126 PO4.9: 3 residues within 4Å: Chain B: N.28, G.53, S.54 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.28, B:S.54, B:S.54, B:S.54 Water bridges: B:Y.51, B:Y.51

1 x SPO: SPHEROIDENE(Non-covalent)

SPO.13: 24 residues within 4Å: Chain B: F.67, I.70, G.71, F.74, W.75, F.85, L.89, W.115, 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.1 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:F.67, B:F.67, B:F.67, B:I.70, B:I.70, B:F.74, B:F.74, B:L.89, B:W.115, B:F.120, B:F.123, B:F.123, B:W.157, B:L.160, B:F.162, B:F.162, B:W.171, B:V.175, B:Y.177, B:Y.177, B:I.179

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

LDA.14: 4 residues within 4Å: Chain B: F.7, L.38, L.39, W.41 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.7, B:L.38, B:L.39 Hydrogen bonds: B:S.8 pi-Cation interactions: B:W.41, B:W.41 LDA.15: 10 residues within 4Å: Chain A: W.151 Chain B: P.200, L.204, A.207, F.208, M.272 Chain C: W.21, L.24 Ligands: BCL.3, LDA.18 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:L.204, B:A.207, C:W.21, C:L.24 Hydrogen bonds: B:P.200 LDA.18: 9 residues within 4Å: Chain B: F.258, W.268 Chain C: I.28, Q.32, Y.40, Q.53, F.56 Ligands: U10.12, LDA.15 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain C Hydrophobic interactions: B:F.258, B:F.258, B:W.268, C:I.28, C:Q.32, C:F.56 Hydrogen bonds: C:Y.40

1 x CDL: CARDIOLIPIN(Non-covalent)

CDL.16: 17 residues within 4Å: Chain A: N.199, P.200 Chain B: G.143, K.144, H.145, W.148, W.155, R.267, I.270, W.271, L.278 Chain C: F.20, I.22, F.23, G.26, L.27, Y.30 25 PLIP interactions: 17 interactions with chain B, 7 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: B:W.148, B:W.155, B:W.155, B:I.270, B:W.271, B:L.278, B:L.278, C:I.22, C:F.23, C:L.27, C:Y.30, C:Y.30 Hydrogen bonds: B:K.144, A:N.199 Water bridges: B:K.144, B:K.144, B:K.144, B:R.267, B:R.267, C:K.62, C:K.62 Salt bridges: B:H.145, B:H.145, B:H.145, B:R.267

1 x K: POTASSIUM ION(Non-covalent)

K.17: 3 residues within 4Å: Chain C: M.134, A.137, F.140 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:M.134, C:A.137

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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