SMTL ID : 8tro.1

Rod from high-resolution phycobilisome quenched by OCP (local refinement)

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

hetero-18-18-1-1-1-1-mer

Ligands

54 x CYC: PHYCOCYANOBILIN(Covalent)

CYC.1: 33 residues within 4Å: Chain 9: R.57, F.60, I.67, Y.74, T.75, S.76, M.79 Chain A: V.59, Y.60, T.66, N.72, N.73, F.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, I.94, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129, A.132 Ligand excluded by PLIP CYC.2: 33 residues within 4Å: Chain B: L.59, F.60, L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, I.89, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, V.127 Chain b: I.246, S.247, G.250, Y.251, V.254, R.255, R.256, S.257 Ligand excluded by PLIP CYC.3: 26 residues within 4Å: Chain A: S.21, L.24, Q.25, F.28 Chain B: A.32, N.35, K.36, I.38, D.39, S.40, N.42, R.43, V.142, N.143, D.144, P.145, I.148, T.149, R.150, G.151, C.153 Chain E: R.32, Q.33, D.145, D.148, E.149 Ligand excluded by PLIP CYC.4: 32 residues within 4Å: Chain B: R.57, F.60, I.67, Y.74, T.75, S.76, M.79 Chain C: V.59, Y.60, T.66, N.72, N.73, F.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, I.94, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129 Ligand excluded by PLIP CYC.5: 26 residues within 4Å: Chain C: S.21, L.24, F.28 Chain D: N.35, K.36, I.38, D.39, S.40, N.42, R.43, V.142, N.143, D.144, P.145, I.148, T.149, R.150, G.151, C.153, I.156 Chain I: R.32, Q.33, D.145, D.148, E.149, S.152 Ligand excluded by PLIP CYC.6: 31 residues within 4Å: Chain D: L.59, F.60, L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, I.89, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, V.127 Chain b: F.265, L.268, N.269, L.272, Q.273, N.276 Ligand excluded by PLIP CYC.7: 32 residues within 4Å: Chain E: V.59, Y.60, T.66, N.72, N.73, F.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, I.94, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129 Chain J: R.57, F.60, I.67, Y.74, T.75, S.76, M.79 Ligand excluded by PLIP CYC.8: 29 residues within 4Å: Chain A: R.32, Q.33, D.145, D.148, E.149 Chain E: S.21, L.24, Q.25, F.28 Chain F: A.32, N.35, K.36, I.38, D.39, S.40, N.42, R.43, V.142, N.143, D.144, P.145, I.148, T.149, R.150, G.151, D.152, C.153, I.156, V.157 Ligand excluded by PLIP CYC.9: 32 residues within 4Å: Chain F: L.59, F.60, L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, I.89, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, V.127 Chain a: F.55, H.56, N.175, I.176, P.179, R.180, Y.181 Ligand excluded by PLIP CYC.10: 32 residues within 4Å: Chain F: R.57, F.60, I.67, Y.74, T.75, S.76, M.79 Chain G: V.59, Y.60, T.66, N.72, N.73, F.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, I.94, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129 Ligand excluded by PLIP CYC.11: 34 residues within 4Å: Chain H: L.59, F.60, L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, I.89, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, V.127 Chain a: L.6, N.100, Y.101, R.120, I.123, A.124, S.126, I.127, A.130 Ligand excluded by PLIP CYC.12: 27 residues within 4Å: Chain 8: R.32, Q.33, D.145, D.148, E.149 Chain G: S.21, L.24, Q.25, F.28 Chain H: N.35, K.36, I.38, D.39, S.40, N.42, R.43, V.142, N.143, D.144, P.145, I.148, T.149, R.150, G.151, D.152, C.153, I.156 Ligand excluded by PLIP CYC.13: 32 residues within 4Å: Chain H: R.57, F.60, I.67, Y.74, T.75, S.76, M.79 Chain I: V.59, Y.60, T.66, N.72, N.73, F.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, I.94, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129 Ligand excluded by PLIP CYC.14: 25 residues within 4Å: Chain C: R.32, Q.33, D.145, D.148, E.149 Chain I: S.21, L.24, F.28 Chain J: A.32, N.35, K.36, I.38, D.39, S.40, N.42, R.43, V.142, N.143, D.144, P.145, I.148, T.149, R.150, G.151, C.153 Ligand excluded by PLIP CYC.15: 35 residues within 4Å: Chain J: L.59, F.60, L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, I.89, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, V.127 Chain a: S.12, Q.13, N.14, R.16, V.17, E.18, G.19, R.161, L.164, R.167 Ligand excluded by PLIP CYC.16: 33 residues within 4Å: Chain K: V.59, Y.60, T.66, N.72, N.73, F.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, I.94, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129, A.132 Chain P: R.57, F.60, I.67, Y.74, T.75, S.76, M.79 Ligand excluded by PLIP CYC.17: 32 residues within 4Å: Chain L: L.59, F.60, L.66, N.72, A.73, R.78, A.81, C.82, R.84, D.85, M.86, I.88, I.89, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, V.127 Chain c: R.24 Chain d: L.27, R.28, Q.29, I.40, R.41, R.42, S.43 Ligand excluded by PLIP CYC.18: 26 residues within 4Å: Chain K: S.21, L.24, Q.25, F.28 Chain L: A.32, N.35, K.36, I.38, D.39, S.40, N.42, R.43, V.142, N.143, D.144, P.145, I.148, T.149, R.150, G.151, C.153 Chain S: R.32, Q.33, D.145, D.148, E.149 Ligand excluded by PLIP CYC.19: 33 residues within 4Å: Chain L: R.57, F.60, I.67, Y.74, T.75, S.76, M.79 Chain M: V.59, Y.60, T.66, N.72, N.73, F.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, I.94, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129, A.132 Ligand excluded by PLIP CYC.20: 27 residues within 4Å: Chain M: S.21, L.24, Q.25, F.28 Chain N: A.32, N.35, K.36, I.38, D.39, S.40, N.42, R.43, V.142, N.143, D.144, P.145, I.148, T.149, R.150, G.151, C.153, I.156 Chain Q: R.32, Q.33, D.145, D.148, E.149 Ligand excluded by PLIP CYC.21: 32 residues within 4Å: Chain N: L.59, F.60, L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, R.91, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, V.127 Chain d: R.18, Y.22, Y.52, M.55, N.56, M.59, R.60 Ligand excluded by PLIP CYC.22: 32 residues within 4Å: Chain N: R.57, F.60, I.67, Y.74, T.75, S.76, M.79 Chain O: V.59, Y.60, T.66, N.72, N.73, F.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, I.94, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129 Ligand excluded by PLIP CYC.23: 26 residues within 4Å: Chain O: S.21, L.24, F.28 Chain P: A.32, N.35, K.36, I.38, D.39, S.40, N.42, R.43, V.142, N.143, D.144, P.145, I.148, T.149, R.150, G.151, C.153, I.156 Chain U: R.32, Q.33, D.145, D.148, E.149 Ligand excluded by PLIP CYC.24: 31 residues within 4Å: Chain P: L.59, F.60, L.66, N.72, A.73, R.78, A.81, C.82, R.84, D.85, M.86, I.88, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, V.127 Chain c: S.57, S.60, L.61, R.63, G.64, E.66 Chain d: L.2, S.5 Ligand excluded by PLIP CYC.25: 33 residues within 4Å: Chain Q: V.59, Y.60, T.66, N.72, N.73, F.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, I.94, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129, A.132 Chain V: R.57, F.60, I.67, Y.74, T.75, S.76, M.79 Ligand excluded by PLIP CYC.26: 35 residues within 4Å: Chain R: L.59, F.60, L.66, N.72, A.73, R.78, A.81, C.82, R.84, D.85, M.86, I.88, I.89, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, V.127 Chain c: T.2, S.3, V.5, S.6, F.154, A.155, T.156, Q.160, K.161, T.162, F.165 Ligand excluded by PLIP CYC.27: 27 residues within 4Å: Chain M: R.32, Q.33, D.145, D.148, E.149 Chain Q: S.21, L.24, Q.25, F.28 Chain R: A.32, N.35, K.36, I.38, D.39, S.40, N.42, R.43, V.142, N.143, D.144, P.145, I.148, T.149, R.150, G.151, D.152, C.153 Ligand excluded by PLIP CYC.28: 32 residues within 4Å: Chain R: R.57, F.60, I.67, Y.74, T.75, S.76, M.79 Chain S: V.59, Y.60, T.66, N.72, N.73, F.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, I.94, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129 Ligand excluded by PLIP CYC.29: 26 residues within 4Å: Chain K: R.32, Q.33, D.145, D.148, E.149 Chain S: S.21, L.24, F.28 Chain T: A.32, N.35, K.36, I.38, D.39, S.40, N.42, R.43, V.142, N.143, D.144, P.145, I.148, T.149, R.150, G.151, C.153, I.156 Ligand excluded by PLIP CYC.30: 33 residues within 4Å: Chain T: L.59, F.60, L.66, N.72, A.73, R.77, R.78, A.81, C.82, D.85, M.86, I.88, I.89, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, V.127 Chain c: R.41, N.46, D.47, H.48, Y.175, A.176, T.177, S.178, R.180 Ligand excluded by PLIP CYC.31: 33 residues within 4Å: Chain T: R.57, F.60, I.67, Y.74, T.75, S.76, M.79 Chain U: V.59, Y.60, T.66, N.72, N.73, F.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, I.94, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129, A.132 Ligand excluded by PLIP CYC.32: 27 residues within 4Å: Chain O: R.32, Q.33, D.145, D.148, E.149 Chain U: S.21, L.24, Q.25, F.28 Chain V: A.32, N.35, K.36, I.38, D.39, S.40, N.42, R.43, V.142, N.143, D.144, P.145, I.148, T.149, R.150, G.151, D.152, C.153 Ligand excluded by PLIP CYC.33: 32 residues within 4Å: Chain V: L.59, F.60, L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, R.91, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, V.127 Chain c: Q.92, N.93, Q.111, I.114, A.115, T.118, Y.121 Ligand excluded by PLIP CYC.34: 32 residues within 4Å: Chain 1: R.57, F.60, I.67, Y.74, T.75, S.76, M.79 Chain W: V.59, Y.60, T.66, N.72, N.73, F.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, I.94, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129 Ligand excluded by PLIP CYC.35: 30 residues within 4Å: Chain X: L.59, F.60, L.66, N.72, A.73, R.78, A.81, C.82, R.84, D.85, M.86, I.88, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, V.127 Chain c: R.219, Y.250, L.253, S.254, L.257, Q.258, N.261 Ligand excluded by PLIP CYC.36: 27 residues within 4Å: Chain 2: R.32, Q.33, D.145, D.148, E.149 Chain W: S.21, L.24, Q.25, F.28 Chain X: A.32, N.35, K.36, I.38, D.39, S.40, N.42, R.43, V.142, N.143, D.144, P.145, I.148, T.149, R.150, G.151, C.153, I.156 Ligand excluded by PLIP CYC.37: 32 residues within 4Å: Chain X: R.57, F.60, I.67, Y.74, T.75, S.76, M.79 Chain Y: V.59, Y.60, T.66, N.72, N.73, F.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, I.94, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129 Ligand excluded by PLIP CYC.38: 31 residues within 4Å: Chain Z: L.59, F.60, L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, V.127 Chain b: G.57, S.60, L.61, T.63, N.64 Chain c: L.211, G.213 Ligand excluded by PLIP CYC.39: 28 residues within 4Å: Chain 6: R.32, Q.33, D.145, D.148, E.149 Chain Y: S.21, L.24, Q.25, F.28 Chain Z: N.35, K.36, I.38, D.39, S.40, N.42, R.43, V.142, N.143, D.144, P.145, I.148, T.149, R.150, G.151, D.152, C.153, I.156, V.157 Ligand excluded by PLIP CYC.40: 33 residues within 4Å: Chain 0: V.59, Y.60, T.66, N.72, N.73, F.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, I.94, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129, A.132 Chain Z: R.57, F.60, I.67, Y.74, T.75, S.76, M.79 Ligand excluded by PLIP CYC.41: 28 residues within 4Å: Chain 0: S.21, L.24, Q.25, F.28 Chain 1: A.32, N.35, K.36, I.38, D.39, S.40, N.42, R.43, V.142, N.143, D.144, P.145, I.148, T.149, R.150, G.151, D.152, C.153, I.156 Chain 4: R.32, Q.33, D.145, D.148, E.149 Ligand excluded by PLIP CYC.42: 32 residues within 4Å: Chain 1: L.59, F.60, L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, V.127 Chain b: R.24 Chain c: G.230, A.231, R.238, V.239, R.240, R.241, G.242 Ligand excluded by PLIP CYC.43: 33 residues within 4Å: Chain 2: V.59, Y.60, T.66, N.72, N.73, F.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, I.94, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129, A.132 Chain 7: R.57, F.60, I.67, Y.74, T.75, S.76, M.79 Ligand excluded by PLIP CYC.44: 25 residues within 4Å: Chain 2: S.21, L.24, Q.25, F.28 Chain 3: N.35, K.36, I.38, D.39, S.40, N.42, R.43, V.142, N.143, D.144, P.145, I.148, T.149, R.150, G.151, C.153 Chain W: R.32, Q.33, D.145, D.148, E.149 Ligand excluded by PLIP CYC.45: 36 residues within 4Å: Chain 3: L.59, F.60, L.66, N.72, A.73, R.78, A.81, C.82, R.84, D.85, M.86, I.88, I.89, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, V.127 Chain b: A.2, I.3, T.4, T.5, A.6, F.153, N.154, N.155, D.159, R.160, T.161, F.164 Ligand excluded by PLIP CYC.46: 32 residues within 4Å: Chain 3: R.57, F.60, I.67, Y.74, T.75, S.76, M.79 Chain 4: V.59, Y.60, T.66, N.72, N.73, F.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, I.94, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129 Ligand excluded by PLIP CYC.47: 25 residues within 4Å: Chain 0: R.32, Q.33, D.145, D.148, E.149 Chain 4: S.21, L.24, F.28 Chain 5: N.35, K.36, I.38, D.39, S.40, N.42, R.43, V.142, N.143, D.144, P.145, I.148, T.149, R.150, G.151, C.153, I.156 Ligand excluded by PLIP CYC.48: 33 residues within 4Å: Chain 5: L.59, F.60, L.66, N.72, A.73, R.77, R.78, A.81, C.82, D.85, M.86, I.88, I.89, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, V.127 Chain b: R.41, N.46, D.47, Y.48, Y.174, A.175, N.176, S.177, S.180 Ligand excluded by PLIP CYC.49: 32 residues within 4Å: Chain 5: R.57, F.60, I.67, Y.74, T.75, S.76, M.79 Chain 6: V.59, Y.60, T.66, N.72, N.73, F.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, I.94, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129 Ligand excluded by PLIP CYC.50: 26 residues within 4Å: Chain 6: S.21, L.24, F.28 Chain 7: N.35, K.36, I.38, D.39, S.40, N.42, R.43, V.142, N.143, D.144, P.145, I.148, T.149, R.150, G.151, D.152, C.153, I.156 Chain Y: R.32, Q.33, D.145, D.148, E.149 Ligand excluded by PLIP CYC.51: 33 residues within 4Å: Chain 7: L.59, F.60, L.66, N.72, A.73, R.77, R.78, A.81, C.82, R.84, D.85, M.86, I.88, I.89, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, V.127 Chain b: F.91, Q.92, T.93, E.111, V.114, I.115, L.118, Y.121 Ligand excluded by PLIP CYC.52: 32 residues within 4Å: Chain 8: V.59, Y.60, T.66, N.72, N.73, F.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, I.94, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129 Chain D: R.57, F.60, I.67, Y.74, T.75, S.76, M.79 Ligand excluded by PLIP CYC.53: 26 residues within 4Å: Chain 8: S.21, L.24, F.28 Chain 9: N.35, K.36, I.38, D.39, S.40, N.42, R.43, V.142, N.143, D.144, P.145, I.148, T.149, R.150, G.151, D.152, C.153, I.156 Chain G: R.32, Q.33, D.145, D.148, E.149 Ligand excluded by PLIP CYC.54: 31 residues within 4Å: Chain 9: L.59, F.60, L.66, N.72, A.73, R.78, A.81, C.82, R.84, D.85, M.86, I.88, I.89, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, V.127 Chain a: V.65, S.68, Q.69, R.71, N.72 Chain b: L.226, G.227 Ligand excluded by PLIP

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

C-phycocyanin alpha subunit: ACEGIKMOQSUWY02468
C-phycocyanin beta subunit: BDFHJLNPRTVXZ13579
Phycobilisome rod-core linker polypeptide CpcG: a
Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1: b
Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2: c
Phycobilisome 8.9 kDa linker polypeptide, phycocyanin-associated, rod: d

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
0

C
2

E
4

G
6

I
8

K
A

M
C

O
E

Q
G

S
I

U
K

W
M

Y
O

0
Q

2
S

4
U

6
W

8
Y

B
1

D
3

F
5

H
7

J
9

L
B

N
D

P
F

R
H

T
J

V
L

X
N

Z
P

1
R

3
T

5
V

7
X

9
Z

a
a

b
b

c
c

d
d

C-phycocyanin alpha subunit

C-phycocyanin beta subunit

Phycobilisome rod-core linker polypeptide CpcG

Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1

Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2

Phycobilisome 8.9 kDa linker polypeptide, phycocyanin-associated, rod

Related Entries With Identical Sequence