SMTL ID : 4ac5.1

Lipidic sponge phase crystal structure of the Bl. viridis reaction centre solved using serial femtosecond crystallography

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 8.20 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 24 residues within 4Å: Chain A: Y.56, K.57, N.58, V.59, K.60, V.61, L.62, F.70, M.74, T.75, I.77, T.78, V.81, S.82, C.87, C.90, H.91, L.96, A.97, Y.104, A.107, R.108, L.111 Ligands: HEM.2 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:Y.56, A:V.59, A:F.70, A:M.74, A:I.77, A:V.81, A:L.96, A:L.96, A:A.107, A:R.108, A:L.111 Hydrogen bonds: A:K.57, A:N.58, A:K.60, A:V.61, A:L.62, A:R.108 pi-Stacking: A:F.70, A:Y.104 Metal complexes: A:H.91 HEM.2: 23 residues within 4Å: Chain A: V.81, Y.89, Y.102, P.103, V.106, A.107, M.110, L.111, M.113, T.114, C.132, C.135, H.136, P.140, L.141, P.142, V.145, L.282, L.289, R.293, P.301, A.303 Ligands: HEM.1 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:V.81, A:P.103, A:A.107, A:M.110, A:L.111, A:L.141, A:P.142, A:V.145, A:L.282, A:P.301, A:A.303 Hydrogen bonds: A:Y.89 Salt bridges: A:R.293, A:R.293 Metal complexes: A:H.136 HEM.3: 25 residues within 4Å: Chain A: V.201, R.202, V.203, V.204, T.229, F.230, M.233, M.234, I.236, S.237, L.240, N.243, C.244, C.247, H.248, F.253, E.254, R.264, A.267, W.268, I.271, R.272 Chain C: Y.163 Chain D: I.190 Ligands: HEM.4 23 PLIP interactions: 21 interactions with chain A, 1 interactions with chain C, 1 interactions with chain D, Hydrophobic interactions: A:V.201, A:V.204, A:T.229, A:F.230, A:M.233, A:I.236, A:L.240, A:F.253, A:F.253, A:E.254, A:A.267, A:W.268, A:I.271, C:Y.163, D:I.190 Hydrogen bonds: A:V.203, A:V.204, A:E.254, A:R.264 Salt bridges: A:R.202, A:R.272 pi-Cation interactions: A:R.264 Metal complexes: A:H.248 HEM.4: 24 residues within 4Å: Chain A: I.117, H.124, V.125, T.128, G.129, V.130, L.194, L.240, F.246, Q.263, I.266, A.267, G.270, I.271, M.273, V.274, D.304, C.305, C.308, H.309, T.313, K.314, P.315 Ligands: HEM.3 12 PLIP interactions: 12 interactions with chain A, Hydrophobic interactions: A:I.117, A:V.130, A:L.194, A:L.240, A:Q.263, A:I.266, A:I.271, A:V.274 Salt bridges: A:K.314, A:K.314 Metal complexes: A:H.124, A:H.309

4 x BCB: BACTERIOCHLOROPHYLL B(Non-covalent)

BCB.5: 30 residues within 4Å: Chain C: F.98, F.122, P.125, M.128, F.129, L.132, V.158, N.159, F.161, G.162, Y.163, W.168, H.169, H.174, S.177, V.178, L.181, F.182, I.241, F.242, G.245, G.248, T.249 Chain D: L.185, Y.196, Y.209 Ligands: BCB.6, BPB.7, BCB.8, BCB.9 18 PLIP interactions: 18 interactions with chain C, Hydrophobic interactions: C:F.98, C:F.98, C:F.122, C:P.125, C:V.158, C:F.161, C:Y.163, C:W.168, C:W.168, C:W.168, C:V.178, C:F.182, C:I.241, C:F.242, C:F.242 Hydrogen bonds: C:S.177 pi-Stacking: C:W.168 Metal complexes: C:H.174 BCB.6: 20 residues within 4Å: Chain C: V.47, I.50, F.129, L.132, F.147, I.151, L.152, H.154, L.155, V.158 Chain D: Y.196, H.201, G.202, I.205, G.206, Y.209, L.213 Ligands: BCB.5, BPB.7, BCB.9 13 PLIP interactions: 7 interactions with chain C, 6 interactions with chain D, Hydrophobic interactions: C:I.50, C:L.132, C:F.147, C:I.151, C:L.155, C:V.158, D:Y.196, D:I.205, D:I.205, D:Y.209, D:L.213 Metal complexes: C:H.154 pi-Stacking: D:Y.209 BCB.8: 21 residues within 4Å: Chain C: H.169, M.175, V.178, S.179, F.182, V.183, M.186 Chain D: M.121, F.155, V.156, I.159, V.174, I.178, W.179, H.181, I.182, L.185 Ligands: BCB.5, BCB.9, BPB.10, NS5.13 14 PLIP interactions: 10 interactions with chain D, 4 interactions with chain C, Hydrophobic interactions: D:F.155, D:V.156, D:I.159, D:V.174, D:I.178, D:I.182, D:L.185, D:L.185, C:V.178, C:V.183 pi-Stacking: D:H.181, C:F.182, C:F.182 pi-Cation interactions: D:H.181 BCB.9: 30 residues within 4Å: Chain C: F.182 Chain D: G.63, A.66, I.67, M.121, S.124, L.125, F.155, V.156, I.159, W.184, L.185, T.186, F.188, S.189, F.195, Y.196, H.201, S.204, I.205, A.208, Y.209, V.275, M.276, A.279, I.283 Ligands: BCB.5, BCB.6, BCB.8, BPB.10 17 PLIP interactions: 16 interactions with chain D, 1 interactions with chain C, Hydrophobic interactions: D:A.66, D:I.67, D:L.125, D:F.155, D:F.155, D:V.156, D:W.184, D:L.185, D:F.188, D:Y.196, D:I.205, D:I.205, D:A.208, D:Y.209, C:F.182 Hydrogen bonds: D:S.204 Metal complexes: D:H.201

2 x BPB: BACTERIOPHEOPHYTIN B(Non-covalent)

BPB.7: 28 residues within 4Å: Chain C: F.42, I.43, G.46, I.50, I.90, C.93, A.94, A.97, F.98, W.101, E.105, V.118, A.121, F.122, P.125, Y.149, G.150, I.151, A.238, F.242 Chain D: Y.209, G.212, L.213, A.216, W.251, I.255 Ligands: BCB.5, BCB.6 15 PLIP interactions: 13 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:I.43, C:I.43, C:I.43, C:I.50, C:I.90, C:A.94, C:W.101, C:A.121, C:F.122, C:F.122, C:P.125, C:Y.149, C:Y.149, D:Y.209, D:L.213 BPB.10: 20 residues within 4Å: Chain C: F.182, M.186, L.190, V.221 Chain D: A.59, F.60, G.63, S.64, I.67, S.124, L.125, W.128, V.132, I.145, N.148, F.149, S.272, M.276 Ligands: BCB.8, BCB.9 9 PLIP interactions: 8 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:A.59, D:F.60, D:F.60, D:I.67, D:W.128, D:W.128, D:N.148, C:F.182 pi-Stacking: D:F.149

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

FE2.11: 5 residues within 4Å: Chain C: H.191, H.231 Chain D: H.218, E.233, H.265 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Metal complexes: C:H.191, C:H.231, D:H.218, D:E.233, D:H.265

1 x MQ7: MENAQUINONE-7(Non-covalent)

MQ7.12: 22 residues within 4Å: Chain C: V.27, Y.30, F.31, V.32, G.36, I.40, W.101, R.104 Chain D: A.217, H.218, T.221, A.247, A.248, W.251, I.255, N.258, A.259, T.260, I.261, V.264, W.267, F.271 19 PLIP interactions: 13 interactions with chain D, 6 interactions with chain C Hydrophobic interactions: D:A.217, D:A.247, D:A.248, D:W.251, D:W.251, D:I.255, D:A.259, D:V.264, D:W.267, D:W.267, D:W.267, D:F.271, C:Y.30, C:Y.30, C:Y.30, C:V.32, C:I.40, C:I.40 Hydrogen bonds: D:A.259

1 x NS5: 15-cis-1,2-dihydroneurosporene(Non-covalent)

NS5.13: 15 residues within 4Å: Chain D: F.89, G.118, L.119, M.121, T.122, L.157, G.160, C.161, W.170, V.174, F.176, G.177, I.178, H.181 Ligands: BCB.8 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.89, D:T.122, D:L.157, D:W.170, D:V.174, D:V.174, D:F.176, D:I.178

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johansson, L.C. et al., Lipidic Phase Membrane Protein Serial Femtosecond Crystallography. Nat.Methods (2012)

Release Date

2012-02-15

Peptides

PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT: A
REACTION CENTER PROTEIN H CHAIN: B
REACTION CENTER PROTEIN L CHAIN: C
REACTION CENTER PROTEIN M CHAIN: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
H

C
L

D
M

Membrane

We predict this structure to be a membrane protein.
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PHOTOSYNTHETIC REACTION CENTER CYTOCHROME C SUBUNIT

REACTION CENTER PROTEIN H CHAIN

REACTION CENTER PROTEIN L CHAIN

REACTION CENTER PROTEIN M CHAIN

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