SMTL ID : 3bsd.1

Light harvesting protein from RC of Chlorobium tepidum

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-trimer

Ligands

3 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: E.195 Chain B: E.195 Chain C: E.195 Ligands: MG.10, MG.19 No protein-ligand interaction detected (PLIP) MG.10: 5 residues within 4Å: Chain A: E.195 Chain B: E.195 Chain C: E.195 Ligands: MG.1, MG.19 No protein-ligand interaction detected (PLIP) MG.19: 5 residues within 4Å: Chain A: E.195 Chain B: E.195 Chain C: E.195 Ligands: MG.1, MG.10 No protein-ligand interaction detected (PLIP)

24 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.2: 25 residues within 4Å: Chain A: V.104, V.106, F.109, H.111, F.113, M.150, V.152, D.158, L.159, T.162, W.163, T.166, I.180, F.183, W.184, I.203, G.219, S.221, W.223 Chain B: S.127, A.129, V.130 Ligands: BCL.3, BCL.7, BCL.18 17 PLIP interactions: 16 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:V.104, A:F.109, A:F.109, A:F.113, A:V.152, A:L.159, A:T.162, A:T.166, A:I.180, A:F.183, A:F.183, A:W.184, A:I.203, A:W.223, A:W.223, B:V.130 Metal complexes: A:H.111 BCL.3: 27 residues within 4Å: Chain A: P.43, C.49, F.71, S.73, V.75, N.80, L.82, I.84, V.104, F.113, F.115, M.150, F.183, W.184, I.186 Chain B: Y.125, V.130, V.134, P.137, I.138, Y.139, M.140, Q.141 Ligands: BCL.2, BCL.4, BCL.7, BCL.8 16 PLIP interactions: 4 interactions with chain B, 11 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: B:Y.139, A:P.43, A:F.71, A:V.75, A:N.80, A:L.82, A:L.82, A:V.104, A:F.113, A:F.115, A:F.183, A:I.186 Hydrogen bonds: B:I.138, B:Y.139, B:Q.141 Metal complexes: H2O.7 BCL.4: 24 residues within 4Å: Chain A: A.12, S.14, Y.16, A.34, A.38, P.39, P.40, A.41, A.189, F.258, S.260, I.265, V.267, H.298, V.301, G.302, N.305, F.307, C.353 Ligands: BCL.3, BCL.5, BCL.6, BCL.7, BCL.8 15 PLIP interactions: 15 interactions with chain A, Hydrophobic interactions: A:A.12, A:A.34, A:A.38, A:A.189, A:F.258, A:I.265, A:V.267, A:V.301, A:V.301, A:N.305, A:F.307, A:F.307 Hydrogen bonds: A:Y.16, A:A.41 Metal complexes: A:H.298 BCL.5: 25 residues within 4Å: Chain A: Y.16, I.18, V.30, A.32, C.49, A.256, G.257, F.258, I.287, L.288, H.290, P.291, P.294, L.295, H.298, L.313, Y.345, W.348, V.349, C.353, F.360, I.362 Ligands: BCL.4, BCL.6, BCL.8 17 PLIP interactions: 17 interactions with chain A, Hydrophobic interactions: A:Y.16, A:Y.16, A:I.18, A:V.30, A:A.32, A:A.256, A:F.258, A:F.258, A:L.288, A:P.291, A:P.294, A:P.294, A:H.298, A:W.348, A:V.349 Hydrogen bonds: A:Y.345 Metal complexes: A:H.290 BCL.6: 23 residues within 4Å: Chain A: V.51, V.55, V.65, I.67, F.71, D.234, S.235, R.238, E.241, L.242, F.243, P.244, V.254, A.256, F.273, P.274, G.275, L.288, P.291 Ligands: BCL.4, BCL.5, BCL.7, BCL.8 14 PLIP interactions: 14 interactions with chain A, Hydrophobic interactions: A:V.51, A:V.55, A:I.67, A:L.242, A:L.242, A:L.242, A:F.243, A:V.254, A:F.273, A:F.273, A:P.274, A:L.288 Salt bridges: A:R.238 Metal complexes: A:L.242 BCL.7: 31 residues within 4Å: Chain A: L.53, V.55, I.67, A.69, F.71, I.84, A.86, I.88, R.96, I.97, S.98, G.117, V.119, Q.144, H.146, I.148, W.184, Q.198, F.225, H.227, S.235, W.239, L.242, A.252, Q.253, V.254 Ligands: BCL.2, BCL.3, BCL.4, BCL.6, BCL.8 16 PLIP interactions: 16 interactions with chain A, Hydrophobic interactions: A:L.53, A:L.53, A:I.67, A:A.69, A:F.71, A:I.84, A:V.119, A:I.148, A:F.225, A:W.239, A:L.242, A:V.254 Hydrogen bonds: A:R.96 Salt bridges: A:R.96 pi-Stacking: A:F.225 Metal complexes: A:H.146 BCL.8: 20 residues within 4Å: Chain A: A.41, F.71, F.185, I.186, P.188, A.189, A.192, Q.198, I.293, P.294, H.297, H.298, M.300, V.301 Chain B: Y.139 Ligands: BCL.3, BCL.4, BCL.5, BCL.6, BCL.7 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B, Hydrophobic interactions: A:F.71, A:F.185, A:F.185, A:P.188, A:P.188, A:A.189, A:A.192, A:P.294, B:Y.139 Hydrogen bonds: A:Q.198 pi-Stacking: A:H.297 Metal complexes: A:H.297 BCL.9: 15 residues within 4Å: Chain A: L.122, Y.124, Y.125, R.126 Chain C: D.161, T.162, G.165, T.166, A.169, T.173, F.176, W.179, I.180, F.183 Ligands: BCL.20 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain A, Hydrophobic interactions: C:T.162, C:T.166, C:A.169, C:F.176, C:F.176, C:F.176, C:I.180, C:F.183, A:Y.124 Metal complexes: A:Y.124 BCL.11: 25 residues within 4Å: Chain B: V.104, V.106, F.109, H.111, F.113, M.150, V.152, D.158, L.159, T.162, W.163, T.166, I.180, F.183, W.184, I.203, G.219, S.221, W.223 Chain C: S.127, A.129, V.130 Ligands: BCL.12, BCL.16, BCL.27 17 PLIP interactions: 16 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:V.104, B:F.109, B:F.109, B:F.113, B:V.152, B:L.159, B:T.162, B:T.166, B:I.180, B:F.183, B:F.183, B:W.184, B:I.203, B:W.223, B:W.223, C:V.130 Metal complexes: B:H.111 BCL.12: 27 residues within 4Å: Chain B: P.43, C.49, F.71, S.73, V.75, N.80, L.82, I.84, V.104, F.113, F.115, M.150, F.183, W.184, I.186 Chain C: Y.125, V.130, V.134, P.137, I.138, Y.139, M.140, Q.141 Ligands: BCL.11, BCL.13, BCL.16, BCL.17 17 PLIP interactions: 11 interactions with chain B, 5 interactions with chain C, 1 Ligand-Water interactions Hydrophobic interactions: B:P.43, B:F.71, B:V.75, B:N.80, B:L.82, B:L.82, B:V.104, B:F.113, B:F.115, B:F.183, B:I.186, C:Y.139 Hydrogen bonds: C:Y.125, C:I.138, C:Y.139, C:Q.141 Metal complexes: H2O.14 BCL.13: 24 residues within 4Å: Chain B: A.12, S.14, Y.16, A.34, A.38, P.39, P.40, A.41, A.189, F.258, S.260, I.265, V.267, H.298, V.301, G.302, N.305, F.307, C.353 Ligands: BCL.12, BCL.14, BCL.15, BCL.16, BCL.17 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:A.12, B:A.34, B:A.38, B:A.189, B:F.258, B:I.265, B:V.267, B:V.301, B:V.301, B:N.305, B:F.307, B:F.307 Hydrogen bonds: B:A.41 Metal complexes: B:H.298 BCL.14: 25 residues within 4Å: Chain B: Y.16, I.18, V.30, A.32, C.49, A.256, G.257, F.258, I.287, L.288, H.290, P.291, P.294, L.295, H.298, L.313, Y.345, W.348, V.349, C.353, F.360, I.362 Ligands: BCL.13, BCL.15, BCL.17 17 PLIP interactions: 17 interactions with chain B, Hydrophobic interactions: B:Y.16, B:Y.16, B:I.18, B:V.30, B:A.32, B:A.256, B:F.258, B:F.258, B:L.288, B:P.291, B:P.294, B:P.294, B:H.298, B:W.348, B:V.349 Hydrogen bonds: B:Y.345 Metal complexes: B:H.290 BCL.15: 23 residues within 4Å: Chain B: V.51, V.55, V.65, I.67, F.71, D.234, S.235, R.238, E.241, L.242, F.243, P.244, V.254, A.256, F.273, P.274, G.275, L.288, P.291 Ligands: BCL.13, BCL.14, BCL.16, BCL.17 14 PLIP interactions: 14 interactions with chain B, Hydrophobic interactions: B:V.51, B:V.55, B:I.67, B:L.242, B:L.242, B:L.242, B:F.243, B:V.254, B:F.273, B:F.273, B:P.274, B:L.288 Salt bridges: B:R.238 Metal complexes: B:L.242 BCL.16: 31 residues within 4Å: Chain B: L.53, V.55, I.67, A.69, F.71, I.84, A.86, I.88, R.96, I.97, S.98, G.117, V.119, Q.144, H.146, I.148, W.184, Q.198, F.225, H.227, S.235, W.239, L.242, A.252, Q.253, V.254 Ligands: BCL.11, BCL.12, BCL.13, BCL.15, BCL.17 16 PLIP interactions: 16 interactions with chain B, Hydrophobic interactions: B:L.53, B:L.53, B:I.67, B:A.69, B:F.71, B:I.84, B:V.119, B:I.148, B:F.225, B:W.239, B:L.242, B:V.254 Hydrogen bonds: B:R.96 Salt bridges: B:R.96 pi-Stacking: B:F.225 Metal complexes: B:H.146 BCL.17: 20 residues within 4Å: Chain B: A.41, F.71, F.185, I.186, P.188, A.189, A.192, Q.198, I.293, P.294, H.297, H.298, M.300, V.301 Chain C: Y.139 Ligands: BCL.12, BCL.13, BCL.14, BCL.15, BCL.16 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain C, Hydrophobic interactions: B:F.71, B:F.185, B:F.185, B:P.188, B:P.188, B:A.189, B:A.192, B:P.294, C:Y.139 Hydrogen bonds: B:Q.198 pi-Stacking: B:H.297 Metal complexes: B:H.297 BCL.18: 15 residues within 4Å: Chain A: D.161, T.162, G.165, T.166, A.169, T.173, F.176, W.179, I.180, F.183 Chain B: L.122, Y.124, Y.125, R.126 Ligands: BCL.2 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: A:T.162, A:T.166, A:A.169, A:F.176, A:F.176, A:F.176, A:I.180, A:F.183, B:Y.124 Metal complexes: B:Y.124 BCL.20: 25 residues within 4Å: Chain A: S.127, A.129, V.130 Chain C: V.104, V.106, F.109, H.111, F.113, M.150, V.152, D.158, L.159, T.162, W.163, T.166, I.180, F.183, W.184, I.203, G.219, S.221, W.223 Ligands: BCL.9, BCL.21, BCL.25 17 PLIP interactions: 16 interactions with chain C, 1 interactions with chain A, Hydrophobic interactions: C:V.104, C:F.109, C:F.109, C:F.113, C:V.152, C:L.159, C:T.162, C:T.166, C:I.180, C:F.183, C:F.183, C:W.184, C:I.203, C:W.223, C:W.223, A:V.130 Metal complexes: C:H.111 BCL.21: 27 residues within 4Å: Chain A: Y.125, V.130, V.134, P.137, I.138, Y.139, M.140, Q.141 Chain C: P.43, C.49, F.71, S.73, V.75, N.80, L.82, I.84, V.104, F.113, F.115, M.150, F.183, W.184, I.186 Ligands: BCL.20, BCL.22, BCL.25, BCL.26 16 PLIP interactions: 11 interactions with chain C, 4 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: C:P.43, C:F.71, C:V.75, C:N.80, C:L.82, C:L.82, C:V.104, C:F.113, C:F.115, C:F.183, C:I.186, A:Y.139 Hydrogen bonds: A:I.138, A:Y.139, A:Q.141 Metal complexes: H2O.21 BCL.22: 24 residues within 4Å: Chain C: A.12, S.14, Y.16, A.34, A.38, P.39, P.40, A.41, A.189, F.258, S.260, I.265, V.267, H.298, V.301, G.302, N.305, F.307, C.353 Ligands: BCL.21, BCL.23, BCL.24, BCL.25, BCL.26 15 PLIP interactions: 15 interactions with chain C, Hydrophobic interactions: C:A.12, C:A.34, C:A.38, C:A.189, C:F.258, C:I.265, C:V.267, C:V.301, C:V.301, C:N.305, C:F.307, C:F.307 Hydrogen bonds: C:Y.16, C:A.41 Metal complexes: C:H.298 BCL.23: 25 residues within 4Å: Chain C: Y.16, I.18, V.30, A.32, C.49, A.256, G.257, F.258, I.287, L.288, H.290, P.291, P.294, L.295, H.298, L.313, Y.345, W.348, V.349, C.353, F.360, I.362 Ligands: BCL.22, BCL.24, BCL.26 17 PLIP interactions: 17 interactions with chain C, Hydrophobic interactions: C:Y.16, C:Y.16, C:I.18, C:V.30, C:A.32, C:A.256, C:F.258, C:F.258, C:L.288, C:P.291, C:P.294, C:P.294, C:H.298, C:W.348, C:V.349 Hydrogen bonds: C:Y.345 Metal complexes: C:H.290 BCL.24: 23 residues within 4Å: Chain C: V.51, V.55, V.65, I.67, F.71, D.234, S.235, R.238, E.241, L.242, F.243, P.244, V.254, A.256, F.273, P.274, G.275, L.288, P.291 Ligands: BCL.22, BCL.23, BCL.25, BCL.26 14 PLIP interactions: 14 interactions with chain C, Hydrophobic interactions: C:V.51, C:V.55, C:I.67, C:L.242, C:L.242, C:L.242, C:F.243, C:V.254, C:F.273, C:F.273, C:P.274, C:L.288 Salt bridges: C:R.238 Metal complexes: C:L.242 BCL.25: 31 residues within 4Å: Chain C: L.53, V.55, I.67, A.69, F.71, I.84, A.86, I.88, R.96, I.97, S.98, G.117, V.119, Q.144, H.146, I.148, W.184, Q.198, F.225, H.227, S.235, W.239, L.242, A.252, Q.253, V.254 Ligands: BCL.20, BCL.21, BCL.22, BCL.24, BCL.26 16 PLIP interactions: 16 interactions with chain C, Hydrophobic interactions: C:L.53, C:L.53, C:I.67, C:A.69, C:F.71, C:I.84, C:V.119, C:I.148, C:F.225, C:W.239, C:L.242, C:V.254 Hydrogen bonds: C:R.96 Salt bridges: C:R.96 pi-Stacking: C:F.225 Metal complexes: C:H.146 BCL.26: 20 residues within 4Å: Chain A: Y.139 Chain C: A.41, F.71, F.185, I.186, P.188, A.189, A.192, Q.198, I.293, P.294, H.297, H.298, M.300, V.301 Ligands: BCL.21, BCL.22, BCL.23, BCL.24, BCL.25 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain A, Hydrophobic interactions: C:F.71, C:F.185, C:F.185, C:P.188, C:P.188, C:A.189, C:A.192, C:P.294, A:Y.139 Hydrogen bonds: C:Q.198 pi-Stacking: C:H.297 Metal complexes: C:H.297 BCL.27: 15 residues within 4Å: Chain B: D.161, T.162, G.165, T.166, A.169, T.173, F.176, W.179, I.180, F.183 Chain C: L.122, Y.124, Y.125, R.126 Ligands: BCL.11 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain C, Hydrophobic interactions: B:T.162, B:T.166, B:A.169, B:F.176, B:F.176, B:F.176, B:I.180, B:F.183, C:Y.124 Metal complexes: C:Y.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ben-Shem, A. et al., Evolution of photosystem I - from symmetry through pseudo-symmetry to asymmetry. Febs Lett. (2004)

Release Date

2008-01-22

Peptides

Bacteriochlorophyll a protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Bacteriochlorophyll a protein

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