- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY 3.10 Å
- Oligo State
- hetero-15-15-1-1-1-1-1-mer
- Ligands
- 48 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)(Covalent)
- 5 x KGD: beta,psi-caroten-4-one(Non-covalent)(Covalent)
KGD.15: 17 residues within 4Å:- Chain A: I.28, V.29, T.32
- Chain H: L.20, L.24, H.27, F.28
- Chain J: S.15, T.16, G.19, M.22, I.26
- Ligands: BCL.2, BCL.12, BCL.13, BCL.16, BCL.19
8 PLIP interactions:3 interactions with chain A, 2 interactions with chain J, 3 interactions with chain H- Hydrophobic interactions: A:I.28, A:V.29, A:T.32, J:T.16, J:I.26, H:L.20, H:H.27, H:F.28
KGD.21: 13 residues within 4Å:- Chain K: H.27
- Chain M: S.15, T.16, L.18, G.19, M.22, I.26
- Chain N: I.28
- Ligands: BCL.17, BCL.18, BCL.20, BCL.22, BCL.26
5 PLIP interactions:1 interactions with chain N, 1 interactions with chain K, 3 interactions with chain M- Hydrophobic interactions: N:I.28, K:H.27, M:T.16, M:M.22, M:I.26
KGD.30: 20 residues within 4Å:- Chain O: L.24, H.27
- Chain Q: V.12, S.15, T.16, G.19, M.22, I.26
- Chain R: V.25, I.28, V.29, T.32, I.33
- Chain S: F.6, S.11
- Ligands: BCL.24, BCL.25, BCL.27, BCL.28, BCL.34
10 PLIP interactions:3 interactions with chain R, 2 interactions with chain S, 2 interactions with chain O, 3 interactions with chain Q- Hydrophobic interactions: R:V.25, R:V.29, R:I.33, S:F.6, O:L.24, O:H.27, Q:V.12, Q:T.16, Q:I.26
- Hydrogen bonds: S:S.11
KGD.32: 13 residues within 4Å:- Chain Q: L.24, H.27
- Chain S: V.12, S.15, T.16, G.19, M.22
- Chain T: V.25, V.29
- Ligands: BCL.27, BCL.28, BCL.31, BCL.51
6 PLIP interactions:2 interactions with chain S, 2 interactions with chain Q, 2 interactions with chain T- Hydrophobic interactions: S:V.12, S:T.16, Q:L.24, Q:H.27, T:V.25, T:V.29
KGD.49: 14 residues within 4Å:- Chain S: H.27, F.28
- Chain W: S.15, T.16, G.19, M.22, I.26
- Chain X: I.28, T.32
- Ligands: BCL.31, BCL.33, BCL.48, BCL.50, BCL.54
4 PLIP interactions:1 interactions with chain X, 2 interactions with chain S, 1 interactions with chain W- Hydrophobic interactions: X:T.32, S:H.27, S:F.28, W:I.26
- 3 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)
BPH.36: 18 residues within 4Å:- Chain U: V.84, Y.87, W.139, Q.143, F.160, V.163, H.192, G.271, V.275
- Chain V: L.199, T.202, L.203, M.207, W.241, M.245
- Ligands: BCL.35, BCL.40, MQE.41
8 PLIP interactions:7 interactions with chain U, 1 interactions with chain V- Hydrophobic interactions: U:V.84, U:Y.87, U:F.160, U:F.160, U:V.163, U:V.275, V:L.199
- Hydrogen bonds: U:Q.143
BPH.38: 18 residues within 4Å:- Chain U: F.207, A.213, T.217, F.220, A.221, L.224
- Chain V: F.52, Y.150, P.164, F.168, I.171, L.172, W.174, T.175
- Ligands: BPH.39, MQE.42, BCL.44, PGV.45
10 PLIP interactions:6 interactions with chain V, 4 interactions with chain U- Hydrophobic interactions: V:F.52, V:F.52, V:Y.150, V:P.164, V:L.172, V:W.174, U:F.207, U:T.217, U:A.221, U:L.224
BPH.39: 14 residues within 4Å:- Chain U: F.220, L.224, H.227, L.254
- Chain V: F.49, W.118, L.122, L.135, F.139, A.142, A.266
- Ligands: BPH.38, MQE.42, BCL.44
6 PLIP interactions:4 interactions with chain V, 2 interactions with chain U- Hydrophobic interactions: V:F.49, V:F.139, V:A.142, V:A.266, U:F.220, U:L.224
- 3 x MQE: 2-methyl-3-[(2E,6E,10E,14E,18E,22E,26E,30E,34E,38E)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,1 4,18,22,26,30,34,38,42-undecaen-1-yl]naphthalene-1,4-dione(Non-covalent)
MQE.37: 19 residues within 4Å:- Chain 6: T.7, M.11, L.14, F.17, L.18, V.21, L.24
- Chain 7: W.40
- Chain U: M.228, H.229, A.232, H.247, W.250, Y.256, S.257, I.258, G.259, E.260
- Chain V: L.31
16 PLIP interactions:8 interactions with chain U, 6 interactions with chain 6, 1 interactions with chain 7, 1 interactions with chain V- Hydrophobic interactions: U:M.228, U:W.250, U:W.250, U:I.258, 6:T.7, 6:L.14, 6:L.14, 6:F.17, 6:V.21, 6:L.24, 7:W.40, V:L.31
- Hydrogen bonds: U:H.229, U:I.258
- pi-Stacking: U:W.250, U:W.250
MQE.41: 18 residues within 4Å:- Chain 8: F.34
- Chain U: F.67, V.84, L.88, W.139, R.142
- Chain V: L.204, M.207, H.208, T.211, W.241, M.245, W.247, A.249, I.254
- Chain Y: V.21, L.25
- Ligands: BPH.36
16 PLIP interactions:6 interactions with chain U, 7 interactions with chain V, 2 interactions with chain Y, 1 interactions with chain 8- Hydrophobic interactions: U:F.67, U:F.67, U:V.84, U:L.88, U:W.139, U:W.139, V:T.211, V:W.241, V:M.245, V:I.254, V:I.254, Y:V.21, Y:L.25, 8:F.34
- Hydrogen bonds: V:H.208, V:A.249
MQE.42: 8 residues within 4Å:- Chain V: I.59, L.60, Y.63, F.78, H.166, G.167
- Ligands: BPH.38, BPH.39
3 PLIP interactions:3 interactions with chain V- Hydrophobic interactions: V:I.59, V:L.60, V:F.78
- 1 x FE: FE (III) ION(Non-covalent)
- 3 x PGV: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE(Non-covalent)(Covalent)
PGV.45: 13 residues within 4Å:- Chain 7: N.191, T.192
- Chain U: Y.208, A.213, W.296, W.299, D.300
- Chain V: E.77, W.79, N.80, F.168, R.169
- Ligands: BPH.38
10 PLIP interactions:5 interactions with chain V, 4 interactions with chain U, 1 interactions with chain 7- Hydrophobic interactions: V:W.79, V:W.79, V:F.168, U:Y.208, U:A.213, U:W.296
- Hydrogen bonds: V:N.80, U:D.300, 7:N.191
- Salt bridges: V:R.169
PGV.46: 14 residues within 4Å:- Chain 6: L.18, P.19, V.22, Y.26
- Chain U: V.137, M.152, M.154, E.155, P.157, I.158, G.161, V.164, S.165
- Chain V: K.217
6 PLIP interactions:1 interactions with chain V, 4 interactions with chain U, 1 interactions with chain 6- Hydrogen bonds: V:K.217, U:M.154, U:E.155
- Hydrophobic interactions: U:V.137, U:V.164, 6:P.19
PGV.47: 10 residues within 4Å:- Chain 7: K.215
- Chain O: V.29, S.32
- Chain V: F.152, L.155, A.156, L.157, G.158, N.159, F.274
2 PLIP interactions:1 interactions with chain O, 1 interactions with chain 7- Hydrogen bonds: O:S.32
- Hydrophobic interactions: 7:K.215
- 4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)(Covalent)
HEM.64: 21 residues within 4Å:- Chain 7: M.78, Y.81, P.88, Q.89, A.90, V.91, Q.92, V.93, I.102, S.103, M.106, V.110, V.116, D.117, C.118, C.121, H.122, F.127, K.139, A.142, R.143
12 PLIP interactions:12 interactions with chain 7,- Hydrophobic interactions: 7:M.78, 7:I.102, 7:V.110, 7:V.116, 7:F.127, 7:K.139, 7:A.142
- Hydrogen bonds: 7:Q.89, 7:Q.92, 7:V.93
- Salt bridges: 7:R.143
- Metal complexes: 7:H.122
HEM.65: 17 residues within 4Å:- Chain 7: L.114, Y.120, K.138, T.141, M.145, T.170, C.171, T.173, C.174, H.175, A.179, A.180, G.181, L.182, M.286, A.287, K.289
15 PLIP interactions:15 interactions with chain 7,- Hydrophobic interactions: 7:L.114, 7:M.145, 7:A.180, 7:L.182, 7:L.182, 7:M.286
- Hydrogen bonds: 7:Y.120, 7:Y.120, 7:G.181, 7:L.182
- Salt bridges: 7:K.138, 7:K.289
- pi-Stacking: 7:H.175, 7:H.175
- Metal complexes: 7:H.175
HEM.66: 19 residues within 4Å:- Chain 7: G.207, G.208, L.209, V.210, V.211, T.212, N.225, Q.226, M.229, M.232, N.233, C.240, C.243, H.244, P.250, K.257, S.260
- Chain U: Y.204
- Chain V: I.180
11 PLIP interactions:9 interactions with chain 7, 1 interactions with chain V, 1 interactions with chain U,- Hydrophobic interactions: 7:M.229, V:I.180, U:Y.204
- Hydrogen bonds: 7:G.207, 7:L.209, 7:V.211, 7:T.212, 7:T.212
- pi-Stacking: 7:H.244
- pi-Cation interactions: 7:K.257
- Metal complexes: 7:H.244
HEM.67: 17 residues within 4Å:- Chain 7: T.157, V.164, G.165, Y.167, I.169, T.173, M.236, Q.256, H.259, M.263, L.264, T.267, C.293, C.296, H.297, N.301, P.303
12 PLIP interactions:12 interactions with chain 7,- Hydrophobic interactions: 7:T.157, 7:T.173, 7:H.259, 7:M.263, 7:L.264, 7:P.303
- Hydrogen bonds: 7:T.157, 7:Y.167, 7:Q.256, 7:N.301
- Salt bridges: 7:H.259
- Metal complexes: 7:H.297
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Xin, J. et al., Carotenoid assembly regulates quinone diffusion and the Roseiflexus castenholzii reaction center-light harvesting complex architecture. Elife (2023)
- Release Date
- 2023-09-20
- Peptides
- Beta subunit of light-harvesting 1: ACEGILNPRTXZ135
Alpha subunit of light-harvesting 1: BDFHJKMOQSWY024
Reaction center protein L chain: U
Reaction center protein M chain: V
SUBUNIT Y: 6
MULTIHEME_CYTC DOMAIN-CONTAINING PROTEIN: 7
SUBUNIT Z: 8 - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
0C
2E
4G
6I
8L
BN
EP
GR
IT
KX
OZ
Q1
S3
U5
WB
1D
3F
5H
7J
9K
AM
DO
FQ
HS
JW
NY
P0
R2
T4
VU
LV
M6
Y7
C8
Z - Membrane
-
We predict this structure to be a membrane protein.
- Coordinates
- PDB Format
- Method
- ELECTRON MICROSCOPY 3.10 Å
- Oligo State
- hetero-15-15-1-1-1-1-1-mer
- Ligands
- 48 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)(Covalent)
- 5 x KGD: beta,psi-caroten-4-one(Non-covalent)(Covalent)
- 3 x BPH: BACTERIOPHEOPHYTIN A(Non-covalent)
- 3 x MQE: 2-methyl-3-[(2E,6E,10E,14E,18E,22E,26E,30E,34E,38E)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,1 4,18,22,26,30,34,38,42-undecaen-1-yl]naphthalene-1,4-dione(Non-covalent)
- 1 x FE: FE (III) ION(Non-covalent)
- 3 x PGV: (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE(Non-covalent)(Covalent)
- 4 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)(Covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Xin, J. et al., Carotenoid assembly regulates quinone diffusion and the Roseiflexus castenholzii reaction center-light harvesting complex architecture. Elife (2023)
- Release Date
- 2023-09-20
- Peptides
- Beta subunit of light-harvesting 1: ACEGILNPRTXZ135
Alpha subunit of light-harvesting 1: BDFHJKMOQSWY024
Reaction center protein L chain: U
Reaction center protein M chain: V
SUBUNIT Y: 6
MULTIHEME_CYTC DOMAIN-CONTAINING PROTEIN: 7
SUBUNIT Z: 8 - SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
0C
2E
4G
6I
8L
BN
EP
GR
IT
KX
OZ
Q1
S3
U5
WB
1D
3F
5H
7J
9K
AM
DO
FQ
HS
JW
NY
P0
R2
T4
VU
LV
M6
Y7
C8
Z - Membrane
-
We predict this structure to be a membrane protein.