SMTL ID : 1kzu.1

INTEGRAL MEMBRANE PERIPHERAL LIGHT HARVESTING COMPLEX FROM RHODOPSEUDOMONAS ACIDOPHILA STRAIN 10050

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-9-9-mer

Ligands

18 x RG1: Rhodopin b-D-glucoside(Non-covalent)

RG1.1: 7 residues within 4Å: Chain A: Y.44 Chain B: A.29, L.32, A.33, A.36 Ligands: BCL.2, BCL.30 Ligand excluded by PLIP RG1.4: 23 residues within 4Å: Chain A: L.20, V.23, I.26 Chain B: L.3, Q.7, L.11, Y.14, V.15, G.18, T.19 Chain C: H.31, L.32, W.45 Chain K: Q.3, K.5, I.6, T.8, V.9 Ligands: BCL.3, BCL.5, BCL.7, BCL.28, BCL.30 Ligand excluded by PLIP RG1.6: 7 residues within 4Å: Chain C: Y.44 Chain D: A.29, L.32, A.33, A.36 Ligands: BCL.5, BCL.7 Ligand excluded by PLIP RG1.9: 23 residues within 4Å: Chain A: Q.3, K.5, I.6, T.8, V.9 Chain C: L.20, V.23, I.26 Chain D: L.3, Q.7, L.11, Y.14, V.15, G.18, T.19 Chain E: H.31, L.32, W.45 Ligands: BCL.3, BCL.5, BCL.8, BCL.10, BCL.12 Ligand excluded by PLIP RG1.11: 7 residues within 4Å: Chain E: Y.44 Chain F: A.29, L.32, A.33, A.36 Ligands: BCL.10, BCL.12 Ligand excluded by PLIP RG1.14: 23 residues within 4Å: Chain C: Q.3, K.5, I.6, T.8, V.9 Chain E: L.20, V.23, I.26 Chain F: L.3, Q.7, L.11, Y.14, V.15, G.18, T.19 Chain M: H.31, L.32, W.45 Ligands: BCL.8, BCL.10, BCL.13, BCL.15, BCL.32 Ligand excluded by PLIP RG1.16: 7 residues within 4Å: Chain G: Y.44 Chain H: A.29, L.32, A.33, A.36 Ligands: BCL.17, BCL.45 Ligand excluded by PLIP RG1.19: 23 residues within 4Å: Chain G: L.20, V.23, I.26 Chain H: L.3, Q.7, L.11, Y.14, V.15, G.18, T.19 Chain I: H.31, L.32, W.45 Chain Q: Q.3, K.5, I.6, T.8, V.9 Ligands: BCL.18, BCL.20, BCL.22, BCL.43, BCL.45 Ligand excluded by PLIP RG1.21: 7 residues within 4Å: Chain I: Y.44 Chain J: A.29, L.32, A.33, A.36 Ligands: BCL.20, BCL.22 Ligand excluded by PLIP RG1.24: 23 residues within 4Å: Chain G: Q.3, K.5, I.6, T.8, V.9 Chain I: L.20, V.23, I.26 Chain J: L.3, Q.7, L.11, Y.14, V.15, G.18, T.19 Chain K: H.31, L.32, W.45 Ligands: BCL.18, BCL.20, BCL.23, BCL.25, BCL.27 Ligand excluded by PLIP RG1.26: 7 residues within 4Å: Chain K: Y.44 Chain L: A.29, L.32, A.33, A.36 Ligands: BCL.25, BCL.27 Ligand excluded by PLIP RG1.29: 23 residues within 4Å: Chain A: H.31, L.32, W.45 Chain I: Q.3, K.5, I.6, T.8, V.9 Chain K: L.20, V.23, I.26 Chain L: L.3, Q.7, L.11, Y.14, V.15, G.18, T.19 Ligands: BCL.2, BCL.23, BCL.25, BCL.28, BCL.30 Ligand excluded by PLIP RG1.31: 7 residues within 4Å: Chain M: Y.44 Chain N: A.29, L.32, A.33, A.36 Ligands: BCL.15, BCL.32 Ligand excluded by PLIP RG1.34: 23 residues within 4Å: Chain E: Q.3, K.5, I.6, T.8, V.9 Chain M: L.20, V.23, I.26 Chain N: L.3, Q.7, L.11, Y.14, V.15, G.18, T.19 Chain O: H.31, L.32, W.45 Ligands: BCL.13, BCL.15, BCL.33, BCL.35, BCL.37 Ligand excluded by PLIP RG1.36: 7 residues within 4Å: Chain O: Y.44 Chain P: A.29, L.32, A.33, A.36 Ligands: BCL.35, BCL.37 Ligand excluded by PLIP RG1.39: 23 residues within 4Å: Chain M: Q.3, K.5, I.6, T.8, V.9 Chain O: L.20, V.23, I.26 Chain P: L.3, Q.7, L.11, Y.14, V.15, G.18, T.19 Chain Q: H.31, L.32, W.45 Ligands: BCL.33, BCL.35, BCL.38, BCL.40, BCL.42 Ligand excluded by PLIP RG1.41: 7 residues within 4Å: Chain Q: Y.44 Chain R: A.29, L.32, A.33, A.36 Ligands: BCL.40, BCL.42 Ligand excluded by PLIP RG1.44: 23 residues within 4Å: Chain G: H.31, L.32, W.45 Chain O: Q.3, K.5, I.6, T.8, V.9 Chain Q: L.20, V.23, I.26 Chain R: L.3, Q.7, L.11, Y.14, V.15, G.18, T.19 Ligands: BCL.17, BCL.38, BCL.40, BCL.43, BCL.45 Ligand excluded by PLIP

27 x BCL: BACTERIOCHLOROPHYLL A(Non-covalent)

BCL.2: 23 residues within 4Å: Chain A: L.20, T.24, A.27, H.31, I.34, W.40, F.41, Y.44, W.45 Chain B: F.22, L.25, A.26, A.29, H.30 Chain K: W.7, V.10, A.18, L.19 Ligands: RG1.1, BCL.5, BCL.28, RG1.29, BCL.30 16 PLIP interactions: 4 interactions with chain K, 10 interactions with chain A, 2 interactions with chain B, Hydrophobic interactions: K:W.7, K:V.10, K:A.18, K:L.19, A:L.20, A:L.20, A:I.34, A:W.40, A:F.41, A:F.41, A:F.41, A:Y.44, A:W.45, B:A.29 Metal complexes: A:H.31 Hydrogen bonds: B:H.30 BCL.3: 15 residues within 4Å: Chain A: M.1, N.2, Q.3 Chain B: I.16, T.19, R.20, L.27, H.30, W.39 Chain C: L.20 Chain D: G.18 Ligands: RG1.4, BCL.5, BCL.7, RG1.9 4 PLIP interactions: 4 interactions with chain B, Hydrophobic interactions: B:R.20, B:L.27, B:W.39 Hydrogen bonds: B:R.20 BCL.5: 23 residues within 4Å: Chain A: V.23, A.27, V.30, H.31, I.34, W.40 Chain B: T.19, F.22, L.23, A.26, H.30, A.33, W.39 Chain C: Y.44, W.45 Chain D: F.22, L.25 Ligands: BCL.2, BCL.3, RG1.4, RG1.6, BCL.7, RG1.9 9 PLIP interactions: 3 interactions with chain A, 5 interactions with chain B, 1 interactions with chain D, Hydrophobic interactions: A:V.30, A:W.40, B:T.19, B:L.23, B:A.33, B:W.39, D:L.25 Hydrogen bonds: A:H.31 Metal complexes: B:H.30 BCL.7: 23 residues within 4Å: Chain A: W.7, V.10, A.18, L.19 Chain C: L.20, T.24, A.27, H.31, I.34, W.40, F.41, Y.44, W.45 Chain D: F.22, L.25, A.26, A.29, H.30 Ligands: BCL.3, RG1.4, BCL.5, RG1.6, BCL.10 16 PLIP interactions: 10 interactions with chain C, 4 interactions with chain A, 2 interactions with chain D, Hydrophobic interactions: C:L.20, C:L.20, C:I.34, C:W.40, C:F.41, C:F.41, C:F.41, C:Y.44, C:W.45, A:W.7, A:V.10, A:A.18, A:L.19, D:A.29 Metal complexes: C:H.31 Hydrogen bonds: D:H.30 BCL.8: 15 residues within 4Å: Chain C: M.1, N.2, Q.3 Chain D: I.16, T.19, R.20, L.27, H.30, W.39 Chain E: L.20 Chain F: G.18 Ligands: RG1.9, BCL.10, BCL.12, RG1.14 4 PLIP interactions: 4 interactions with chain D, Hydrophobic interactions: D:R.20, D:L.27, D:W.39 Hydrogen bonds: D:R.20 BCL.10: 23 residues within 4Å: Chain C: V.23, A.27, V.30, H.31, I.34, W.40 Chain D: T.19, F.22, L.23, A.26, H.30, A.33, W.39 Chain E: Y.44, W.45 Chain F: F.22, L.25 Ligands: BCL.7, BCL.8, RG1.9, RG1.11, BCL.12, RG1.14 9 PLIP interactions: 5 interactions with chain D, 1 interactions with chain F, 3 interactions with chain C, Hydrophobic interactions: D:T.19, D:L.23, D:A.33, D:W.39, F:L.25, C:V.30, C:W.40 Metal complexes: D:H.30 Hydrogen bonds: C:H.31 BCL.12: 23 residues within 4Å: Chain C: W.7, V.10, A.18, L.19 Chain E: L.20, T.24, A.27, H.31, I.34, W.40, F.41, Y.44, W.45 Chain F: F.22, L.25, A.26, A.29, H.30 Ligands: BCL.8, RG1.9, BCL.10, RG1.11, BCL.15 16 PLIP interactions: 4 interactions with chain C, 2 interactions with chain F, 10 interactions with chain E, Hydrophobic interactions: C:W.7, C:V.10, C:A.18, C:L.19, F:A.29, E:L.20, E:L.20, E:I.34, E:W.40, E:F.41, E:F.41, E:F.41, E:Y.44, E:W.45 Hydrogen bonds: F:H.30 Metal complexes: E:H.31 BCL.13: 15 residues within 4Å: Chain E: M.1, N.2, Q.3 Chain F: I.16, T.19, R.20, L.27, H.30, W.39 Chain M: L.20 Chain N: G.18 Ligands: RG1.14, BCL.15, BCL.32, RG1.34 4 PLIP interactions: 4 interactions with chain F, Hydrophobic interactions: F:R.20, F:L.27, F:W.39 Hydrogen bonds: F:R.20 BCL.15: 23 residues within 4Å: Chain E: V.23, A.27, V.30, H.31, I.34, W.40 Chain F: T.19, F.22, L.23, A.26, H.30, A.33, W.39 Chain M: Y.44, W.45 Chain N: F.22, L.25 Ligands: BCL.12, BCL.13, RG1.14, RG1.31, BCL.32, RG1.34 9 PLIP interactions: 5 interactions with chain F, 3 interactions with chain E, 1 interactions with chain N, Hydrophobic interactions: F:T.19, F:L.23, F:A.33, F:W.39, E:V.30, E:W.40, N:L.25 Metal complexes: F:H.30 Hydrogen bonds: E:H.31 BCL.17: 23 residues within 4Å: Chain G: L.20, T.24, A.27, H.31, I.34, W.40, F.41, Y.44, W.45 Chain H: F.22, L.25, A.26, A.29, H.30 Chain Q: W.7, V.10, A.18, L.19 Ligands: RG1.16, BCL.20, BCL.43, RG1.44, BCL.45 16 PLIP interactions: 4 interactions with chain Q, 10 interactions with chain G, 2 interactions with chain H, Hydrophobic interactions: Q:W.7, Q:V.10, Q:A.18, Q:L.19, G:L.20, G:L.20, G:I.34, G:W.40, G:F.41, G:F.41, G:F.41, G:Y.44, G:W.45, H:A.29 Metal complexes: G:H.31 Hydrogen bonds: H:H.30 BCL.18: 15 residues within 4Å: Chain G: M.1, N.2, Q.3 Chain H: I.16, T.19, R.20, L.27, H.30, W.39 Chain I: L.20 Chain J: G.18 Ligands: RG1.19, BCL.20, BCL.22, RG1.24 4 PLIP interactions: 4 interactions with chain H, Hydrophobic interactions: H:R.20, H:L.27, H:W.39 Hydrogen bonds: H:R.20 BCL.20: 23 residues within 4Å: Chain G: V.23, A.27, V.30, H.31, I.34, W.40 Chain H: T.19, F.22, L.23, A.26, H.30, A.33, W.39 Chain I: Y.44, W.45 Chain J: F.22, L.25 Ligands: BCL.17, BCL.18, RG1.19, RG1.21, BCL.22, RG1.24 9 PLIP interactions: 5 interactions with chain H, 3 interactions with chain G, 1 interactions with chain J, Hydrophobic interactions: H:T.19, H:L.23, H:A.33, H:W.39, G:V.30, G:W.40, J:L.25 Metal complexes: H:H.30 Hydrogen bonds: G:H.31 BCL.22: 23 residues within 4Å: Chain G: W.7, V.10, A.18, L.19 Chain I: L.20, T.24, A.27, H.31, I.34, W.40, F.41, Y.44, W.45 Chain J: F.22, L.25, A.26, A.29, H.30 Ligands: BCL.18, RG1.19, BCL.20, RG1.21, BCL.25 16 PLIP interactions: 2 interactions with chain J, 10 interactions with chain I, 4 interactions with chain G, Hydrophobic interactions: J:A.29, I:L.20, I:L.20, I:I.34, I:W.40, I:F.41, I:F.41, I:F.41, I:Y.44, I:W.45, G:W.7, G:V.10, G:A.18, G:L.19 Hydrogen bonds: J:H.30 Metal complexes: I:H.31 BCL.23: 15 residues within 4Å: Chain I: M.1, N.2, Q.3 Chain J: I.16, T.19, R.20, L.27, H.30, W.39 Chain K: L.20 Chain L: G.18 Ligands: RG1.24, BCL.25, BCL.27, RG1.29 4 PLIP interactions: 4 interactions with chain J, Hydrophobic interactions: J:R.20, J:L.27, J:W.39 Hydrogen bonds: J:R.20 BCL.25: 23 residues within 4Å: Chain I: V.23, A.27, V.30, H.31, I.34, W.40 Chain J: T.19, F.22, L.23, A.26, H.30, A.33, W.39 Chain K: Y.44, W.45 Chain L: F.22, L.25 Ligands: BCL.22, BCL.23, RG1.24, RG1.26, BCL.27, RG1.29 9 PLIP interactions: 5 interactions with chain J, 3 interactions with chain I, 1 interactions with chain L, Hydrophobic interactions: J:T.19, J:L.23, J:A.33, J:W.39, I:V.30, I:W.40, L:L.25 Metal complexes: J:H.30 Hydrogen bonds: I:H.31 BCL.27: 23 residues within 4Å: Chain I: W.7, V.10, A.18, L.19 Chain K: L.20, T.24, A.27, H.31, I.34, W.40, F.41, Y.44, W.45 Chain L: F.22, L.25, A.26, A.29, H.30 Ligands: BCL.23, RG1.24, BCL.25, RG1.26, BCL.30 16 PLIP interactions: 4 interactions with chain I, 10 interactions with chain K, 2 interactions with chain L, Hydrophobic interactions: I:W.7, I:V.10, I:A.18, I:L.19, K:L.20, K:L.20, K:I.34, K:W.40, K:F.41, K:F.41, K:F.41, K:Y.44, K:W.45, L:A.29 Metal complexes: K:H.31 Hydrogen bonds: L:H.30 BCL.28: 15 residues within 4Å: Chain A: L.20 Chain B: G.18 Chain K: M.1, N.2, Q.3 Chain L: I.16, T.19, R.20, L.27, H.30, W.39 Ligands: BCL.2, RG1.4, RG1.29, BCL.30 4 PLIP interactions: 4 interactions with chain L, Hydrophobic interactions: L:R.20, L:L.27, L:W.39 Hydrogen bonds: L:R.20 BCL.30: 23 residues within 4Å: Chain A: Y.44, W.45 Chain B: F.22, L.25 Chain K: V.23, A.27, V.30, H.31, I.34, W.40 Chain L: T.19, F.22, L.23, A.26, H.30, A.33, W.39 Ligands: RG1.1, BCL.2, RG1.4, BCL.27, BCL.28, RG1.29 9 PLIP interactions: 5 interactions with chain L, 3 interactions with chain K, 1 interactions with chain B, Hydrophobic interactions: L:T.19, L:L.23, L:A.33, L:W.39, K:V.30, K:W.40, B:L.25 Metal complexes: L:H.30 Hydrogen bonds: K:H.31 BCL.32: 23 residues within 4Å: Chain E: W.7, V.10, A.18, L.19 Chain M: L.20, T.24, A.27, H.31, I.34, W.40, F.41, Y.44, W.45 Chain N: F.22, L.25, A.26, A.29, H.30 Ligands: BCL.13, RG1.14, BCL.15, RG1.31, BCL.35 16 PLIP interactions: 4 interactions with chain E, 10 interactions with chain M, 2 interactions with chain N, Hydrophobic interactions: E:W.7, E:V.10, E:A.18, E:L.19, M:L.20, M:L.20, M:I.34, M:W.40, M:F.41, M:F.41, M:F.41, M:Y.44, M:W.45, N:A.29 Metal complexes: M:H.31 Hydrogen bonds: N:H.30 BCL.33: 15 residues within 4Å: Chain M: M.1, N.2, Q.3 Chain N: I.16, T.19, R.20, L.27, H.30, W.39 Chain O: L.20 Chain P: G.18 Ligands: RG1.34, BCL.35, BCL.37, RG1.39 4 PLIP interactions: 4 interactions with chain N, Hydrophobic interactions: N:R.20, N:L.27, N:W.39 Hydrogen bonds: N:R.20 BCL.35: 23 residues within 4Å: Chain M: V.23, A.27, V.30, H.31, I.34, W.40 Chain N: T.19, F.22, L.23, A.26, H.30, A.33, W.39 Chain O: Y.44, W.45 Chain P: F.22, L.25 Ligands: BCL.32, BCL.33, RG1.34, RG1.36, BCL.37, RG1.39 9 PLIP interactions: 5 interactions with chain N, 1 interactions with chain P, 3 interactions with chain M, Hydrophobic interactions: N:T.19, N:L.23, N:A.33, N:W.39, P:L.25, M:V.30, M:W.40 Metal complexes: N:H.30 Hydrogen bonds: M:H.31 BCL.37: 23 residues within 4Å: Chain M: W.7, V.10, A.18, L.19 Chain O: L.20, T.24, A.27, H.31, I.34, W.40, F.41, Y.44, W.45 Chain P: F.22, L.25, A.26, A.29, H.30 Ligands: BCL.33, RG1.34, BCL.35, RG1.36, BCL.40 16 PLIP interactions: 4 interactions with chain M, 10 interactions with chain O, 2 interactions with chain P, Hydrophobic interactions: M:W.7, M:V.10, M:A.18, M:L.19, O:L.20, O:L.20, O:I.34, O:W.40, O:F.41, O:F.41, O:F.41, O:Y.44, O:W.45, P:A.29 Metal complexes: O:H.31 Hydrogen bonds: P:H.30 BCL.38: 15 residues within 4Å: Chain O: M.1, N.2, Q.3 Chain P: I.16, T.19, R.20, L.27, H.30, W.39 Chain Q: L.20 Chain R: G.18 Ligands: RG1.39, BCL.40, BCL.42, RG1.44 4 PLIP interactions: 4 interactions with chain P, Hydrophobic interactions: P:R.20, P:L.27, P:W.39 Hydrogen bonds: P:R.20 BCL.40: 23 residues within 4Å: Chain O: V.23, A.27, V.30, H.31, I.34, W.40 Chain P: T.19, F.22, L.23, A.26, H.30, A.33, W.39 Chain Q: Y.44, W.45 Chain R: F.22, L.25 Ligands: BCL.37, BCL.38, RG1.39, RG1.41, BCL.42, RG1.44 9 PLIP interactions: 5 interactions with chain P, 3 interactions with chain O, 1 interactions with chain R, Hydrophobic interactions: P:T.19, P:L.23, P:A.33, P:W.39, O:V.30, O:W.40, R:L.25 Metal complexes: P:H.30 Hydrogen bonds: O:H.31 BCL.42: 23 residues within 4Å: Chain O: W.7, V.10, A.18, L.19 Chain Q: L.20, T.24, A.27, H.31, I.34, W.40, F.41, Y.44, W.45 Chain R: F.22, L.25, A.26, A.29, H.30 Ligands: BCL.38, RG1.39, BCL.40, RG1.41, BCL.45 16 PLIP interactions: 10 interactions with chain Q, 4 interactions with chain O, 2 interactions with chain R, Hydrophobic interactions: Q:L.20, Q:L.20, Q:I.34, Q:W.40, Q:F.41, Q:F.41, Q:F.41, Q:Y.44, Q:W.45, O:W.7, O:V.10, O:A.18, O:L.19, R:A.29 Metal complexes: Q:H.31 Hydrogen bonds: R:H.30 BCL.43: 15 residues within 4Å: Chain G: L.20 Chain H: G.18 Chain Q: M.1, N.2, Q.3 Chain R: I.16, T.19, R.20, L.27, H.30, W.39 Ligands: BCL.17, RG1.19, RG1.44, BCL.45 4 PLIP interactions: 4 interactions with chain R, Hydrophobic interactions: R:R.20, R:L.27, R:W.39 Hydrogen bonds: R:R.20 BCL.45: 23 residues within 4Å: Chain G: Y.44, W.45 Chain H: F.22, L.25 Chain Q: V.23, A.27, V.30, H.31, I.34, W.40 Chain R: T.19, F.22, L.23, A.26, H.30, A.33, W.39 Ligands: RG1.16, BCL.17, RG1.19, BCL.42, BCL.43, RG1.44 9 PLIP interactions: 3 interactions with chain Q, 5 interactions with chain R, 1 interactions with chain H, Hydrophobic interactions: Q:V.30, Q:W.40, R:T.19, R:L.23, R:A.33, R:W.39, H:L.25 Hydrogen bonds: Q:H.31 Metal complexes: R:H.30

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prince, S.M. et al., Apoprotein structure in the LH2 complex from Rhodopseudomonas acidophila strain 10050: modular assembly and protein pigment interactions. J.Mol.Biol. (1997)

Release Date

1997-04-01

Peptides

LIGHT HARVESTING PROTEIN B-800/850: ACEGIKMOQ
LIGHT HARVESTING PROTEIN B-800/850: BDFHJLNPR

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
D

E
G

G
A

I
D

K
G

M
A

O
D

Q
G

B
B

D
E

F
H

H
B

J
E

L
H

N
B

P
E

R
H

Membrane

We predict this structure to be a membrane protein.
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LIGHT HARVESTING PROTEIN B-800/850

LIGHT HARVESTING PROTEIN B-800/850

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