SMTL ID : 8tpj.1

Top cylinder bound to OCP from high-resolution phycobilisome quenched by OCP (local refinement)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-1-2-1-6-6-4-mer

Ligands

1 x 45D: beta,beta-carotene-4,4'-dione(Non-covalent)

45D.1: 39 residues within 4Å: Chain B: E.34, L.37, A.38, I.40, W.41, A.43, Y.44, M.47, T.52, I.53, A.54, A.55, P.56, A.58, A.59, T.80, M.83, C.84, N.104, L.107, G.108, W.110, Y.111, L.113, G.114, M.117, I.125, P.126, Y.129, I.151, L.154, R.155, E.174, P.175, V.176, V.177 Chain E: P.68, G.69, Y.73 28 PLIP interactions: 25 interactions with chain B, 3 interactions with chain E Hydrophobic interactions: B:E.34, B:L.37, B:L.37, B:L.37, B:A.38, B:I.40, B:W.41, B:Y.44, B:T.52, B:A.54, B:A.55, B:A.58, B:T.80, B:L.107, B:L.107, B:L.107, B:W.110, B:W.110, B:I.125, B:Y.129, B:Y.129, B:I.151, B:L.154, B:V.176, E:P.68, E:Y.73 Hydrogen bonds: B:V.177, E:G.69

12 x CYC: PHYCOCYANOBILIN(Covalent)

CYC.2: 32 residues within 4Å: Chain E: L.58, I.65, N.71, A.72, M.77, T.80, C.81, R.83, D.84, M.85, Y.87, Y.88, R.90, L.91, I.107, G.108, V.112, M.115, Y.116, L.119, T.121, P.122, A.125, V.126, S.129 Chain J: L.61, Y.62, T.66, Y.73, T.74, T.75, Y.78 34 PLIP interactions: 19 interactions with chain E, 12 interactions with chain J, 3 interactions with chain R Hydrophobic interactions: E:L.58, E:I.65, E:T.80, E:Y.87, E:Y.88, E:L.119, E:T.121, E:A.125, E:V.126, J:L.61, J:Y.62, J:Y.73, J:T.75, J:Y.78 Hydrogen bonds: E:N.71, E:A.72, E:R.83, E:D.84, E:T.121, J:Y.62, J:Y.62, J:Y.62, J:T.66, J:T.74 Water bridges: E:R.83, E:Y.87, E:Y.87, J:K.53, J:T.66, R:R.249, R:R.249, R:R.249 Salt bridges: E:R.83 pi-Cation interactions: E:R.83 CYC.3: 32 residues within 4Å: Chain A: K.732, A.762, S.765, K.766, S.768, N.769, E.771 Chain F: L.60, V.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.88, Y.91, R.107, V.108, L.112, T.115, Y.116, L.119, V.121, P.122, S.125, T.126, A.129 31 PLIP interactions: 24 interactions with chain F, 7 interactions with chain A Hydrophobic interactions: F:R.77, F:A.80, F:L.85, F:Y.87, F:Y.88, F:Y.91, F:T.115, F:L.119, F:V.121, F:V.121, F:P.122, A:N.769 Hydrogen bonds: F:R.83, F:Y.116, F:Y.116, A:S.765, A:S.765, A:S.765, A:K.766, A:S.768 Water bridges: F:R.76, F:R.76, F:R.76, F:R.76, F:R.83, F:R.83, A:K.732 Salt bridges: F:R.76, F:R.77, F:R.83 pi-Cation interactions: F:R.83 CYC.4: 32 residues within 4Å: Chain F: L.61, Y.62, T.66, Y.73, T.74, T.75, Y.78 Chain G: L.58, I.65, N.71, A.72, M.77, T.80, C.81, R.83, D.84, M.85, Y.87, Y.88, R.90, L.91, I.107, G.108, M.115, Y.116, L.119, T.121, P.122, A.125, V.126, S.129 Chain Q: R.249 26 PLIP interactions: 10 interactions with chain F, 15 interactions with chain G, 1 interactions with chain Q Hydrophobic interactions: F:L.61, F:Y.62, F:Y.73, F:T.75, F:Y.78, G:I.65, G:T.80, G:Y.87, G:Y.88, G:L.119, G:T.121, G:A.125, G:V.126 Hydrogen bonds: F:Y.62, F:Y.62, F:Y.62, F:T.74, G:N.71, G:R.83, G:D.84, G:T.121 Salt bridges: F:K.53, G:R.83 pi-Stacking: G:Y.87 pi-Cation interactions: G:R.83 Water bridges: Q:R.249 CYC.5: 32 residues within 4Å: Chain D: P.11, S.12, R.17, R.20, E.21, L.22, T.25 Chain H: L.60, V.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.88, Y.91, R.107, V.108, L.112, T.115, Y.116, L.119, V.121, P.122, S.125, T.126, A.129 30 PLIP interactions: 7 interactions with chain D, 23 interactions with chain H Hydrophobic interactions: D:L.22, D:L.22, H:L.60, H:R.77, H:A.80, H:L.85, H:Y.87, H:Y.87, H:Y.87, H:Y.88, H:Y.91, H:T.115, H:Y.116, H:L.119, H:V.121, H:V.121, H:A.129 Hydrogen bonds: D:E.21, D:L.22, H:R.83, H:D.84 Water bridges: D:S.12, D:S.12, H:Y.87, H:Y.87 Salt bridges: D:R.17, H:R.76, H:R.77, H:R.83 pi-Cation interactions: H:R.83 CYC.6: 32 residues within 4Å: Chain H: L.61, Y.62, T.66, Y.73, T.74, T.75, Y.78 Chain I: L.58, F.59, I.65, N.71, A.72, M.77, T.80, C.81, R.83, D.84, M.85, Y.87, Y.88, R.90, L.91, I.107, G.108, M.115, Y.116, L.119, T.121, P.122, A.125, V.126, S.129 31 PLIP interactions: 20 interactions with chain I, 11 interactions with chain H Hydrophobic interactions: I:L.58, I:T.80, I:Y.87, I:Y.88, I:L.119, I:L.119, I:T.121, I:A.125, I:V.126, H:L.61, H:Y.62, H:Y.73, H:Y.78 Hydrogen bonds: I:N.71, I:A.72, I:R.83, I:D.84, H:Y.62, H:Y.62, H:Y.62, H:T.66, H:T.74 Water bridges: I:N.71, I:R.83, I:R.83, I:Y.87, H:T.66, H:T.66 Salt bridges: I:R.83 pi-Stacking: I:Y.87 pi-Cation interactions: I:R.83 CYC.7: 34 residues within 4Å: Chain D: R.2, F.4, Y.33, W.36, F.37, Q.40, Q.41, M.44, G.61 Chain J: L.60, V.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.88, Y.91, R.107, V.108, L.112, T.115, Y.116, L.119, V.121, P.122, S.125, T.126, A.129 25 PLIP interactions: 10 interactions with chain D, 15 interactions with chain J Hydrophobic interactions: D:Y.33, D:F.37, J:R.77, J:A.80, J:L.85, J:Y.87, J:Y.88, J:T.115, J:Y.116, J:V.121, J:V.121 Hydrogen bonds: D:Y.33, D:Q.40, J:R.83, J:D.84 Water bridges: D:R.2, D:R.2, D:Y.33, D:Y.33, D:T.62 Salt bridges: D:R.2, J:R.76, J:R.77, J:R.83 pi-Cation interactions: J:R.83 CYC.8: 34 residues within 4Å: Chain K: L.58, F.59, I.65, N.71, A.72, M.77, T.80, C.81, R.83, D.84, M.85, Y.87, Y.88, R.90, L.91, I.107, G.108, V.112, M.115, Y.116, L.119, T.121, P.122, A.125, V.126, S.129 Chain L: L.61, Y.62, T.66, Y.73, T.74, T.75, Y.78 Chain T: R.201 28 PLIP interactions: 16 interactions with chain K, 11 interactions with chain L, 1 interactions with chain T Hydrophobic interactions: K:L.58, K:I.65, K:T.80, K:Y.87, K:Y.88, K:I.107, K:L.119, K:A.125, L:L.61, L:Y.62, L:Y.73, L:T.75, L:Y.78 Hydrogen bonds: K:N.71, K:A.72, K:R.83, K:D.84, K:T.121, L:Y.62, L:Y.62, L:Y.62, L:T.66, L:T.74 Water bridges: K:Y.87, L:T.66 Salt bridges: K:R.83, T:R.201 pi-Cation interactions: K:R.83 CYC.9: 28 residues within 4Å: Chain A: R.749, L.876, T.877, K.878 Chain L: L.60, V.65, N.71, M.72, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.88, Y.91, R.107, V.108, L.112, T.115, Y.116, L.119, V.121, P.122, S.125, T.126, A.129 29 PLIP interactions: 8 interactions with chain A, 21 interactions with chain L Hydrophobic interactions: A:L.876, A:T.877, L:L.60, L:R.77, L:A.80, L:L.85, L:Y.87, L:Y.88, L:Y.91, L:T.115, L:L.119, L:V.121, L:V.121, L:P.122 Water bridges: A:R.749, A:R.749, A:K.878, L:R.77, L:R.77, L:Y.87 Salt bridges: A:R.749, A:K.878, A:K.878, L:R.77, L:R.83 Hydrogen bonds: L:R.83, L:D.84, L:Y.87 pi-Cation interactions: L:R.83 CYC.10: 32 residues within 4Å: Chain M: L.58, F.59, I.65, N.71, A.72, M.77, T.80, C.81, R.83, D.84, M.85, Y.87, Y.88, L.91, I.107, G.108, M.115, Y.116, L.119, T.121, P.122, A.125, V.126, S.129 Chain N: L.61, Y.62, S.63, T.66, Y.73, T.74, T.75, Y.78 31 PLIP interactions: 19 interactions with chain M, 12 interactions with chain N Hydrophobic interactions: M:L.58, M:I.65, M:T.80, M:Y.88, M:L.119, M:L.119, M:T.121, M:A.125, M:V.126, N:L.61, N:Y.62, N:Y.73, N:Y.78 Hydrogen bonds: M:N.71, M:A.72, M:R.83, M:D.84, N:Y.62, N:Y.62, N:Y.62, N:T.66, N:T.74 Water bridges: M:N.71, M:R.83, M:R.83, N:K.53, N:T.66, N:T.66 Salt bridges: M:R.83 pi-Stacking: M:Y.87 pi-Cation interactions: M:R.83 CYC.11: 36 residues within 4Å: Chain A: G.713, V.714, R.718, F.858, P.859, T.860, L.861, P.862, A.863, F.866, P.867 Chain N: L.60, V.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.88, Y.91, R.107, V.108, L.112, T.115, Y.116, L.119, V.121, P.122, S.125, T.126, A.129 28 PLIP interactions: 15 interactions with chain N, 13 interactions with chain A Hydrophobic interactions: N:L.60, N:R.77, N:A.80, N:L.85, N:Y.88, N:Y.91, N:L.112, N:T.115, N:L.119, A:V.714, A:F.866, A:F.866, A:F.866 Hydrogen bonds: N:R.83, N:D.84, A:V.714, A:T.860, A:T.860 Water bridges: N:R.83, A:R.718, A:R.718, A:A.864, A:A.864 Salt bridges: N:R.83, A:R.718, A:R.718 pi-Stacking: N:Y.87 pi-Cation interactions: N:R.83 CYC.12: 33 residues within 4Å: Chain O: L.58, F.59, I.65, N.71, A.72, M.77, T.80, C.81, R.83, D.84, M.85, Y.87, Y.88, L.91, I.107, G.108, M.115, Y.116, L.119, T.121, P.122, A.125, V.126, S.129 Chain P: L.61, Y.62, S.63, T.66, Y.73, T.74, T.75, Y.78 Chain S: R.201 21 PLIP interactions: 10 interactions with chain O, 9 interactions with chain P, 2 interactions with chain S Hydrophobic interactions: O:L.58, O:Y.87, O:Y.88, O:A.125, O:V.126, P:L.61, P:Y.62, P:Y.78 Hydrogen bonds: O:N.71, O:R.83, O:D.84, P:Y.62, P:Y.62, P:Y.62, P:T.66, P:T.74 Salt bridges: O:R.83, S:R.201 pi-Cation interactions: O:R.83 Water bridges: P:S.63, S:R.201 CYC.13: 36 residues within 4Å: Chain A: P.796, N.797, T.798, Q.816, I.819, Q.820, N.823, Q.824, P.886, S.887, K.893 Chain P: L.60, V.65, N.71, M.72, R.76, R.77, A.80, C.81, R.83, D.84, L.85, Y.87, Y.88, Y.91, R.107, V.108, L.112, T.115, Y.116, L.119, V.121, P.122, S.125, T.126, A.129 34 PLIP interactions: 24 interactions with chain P, 10 interactions with chain A Hydrophobic interactions: P:R.77, P:A.80, P:L.85, P:Y.87, P:Y.88, P:Y.91, P:L.112, P:T.115, P:L.119, P:V.121, P:V.121, P:P.122, P:A.129, A:I.819 Hydrogen bonds: P:D.84, A:N.797, A:T.798, A:Q.820, A:N.823, A:Q.824 Water bridges: P:R.76, P:R.76, P:R.76, P:R.76, P:R.76, P:R.77, P:R.83, P:R.83, A:T.798, A:Q.816, A:N.823 Salt bridges: P:R.76, P:R.83, A:K.893

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sauer, P.V. et al., Structural and quantum chemical basis for OCP-mediated quenching of phycobilisomes. Sci Adv (2024)

Release Date

2024-04-17

Peptides

Phycobiliprotein ApcE: A
Orange carotenoid-binding protein: BC
Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core: D
Allophycocyanin alpha chain: EGIKMO
Allophycocyanin beta chain: FHJLNP
Phycobilisome rod-core linker polypeptide CpcG: QRST

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
b

D
C

E
D

G
F

I
H

K
J

M
L

O
N

F
E

H
G

J
I

L
K

N
M

P
O

Q
P

R
Q

S
R

T
S

Phycobiliprotein ApcE

Orange carotenoid-binding protein

Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core

Allophycocyanin alpha chain

Allophycocyanin beta chain

Phycobilisome rod-core linker polypeptide CpcG

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