SMTL ID : 6yx8.1

The structure of allophycocyanin from cyanobacterium Nostoc sp. WR13, the C2221 crystal form.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

hetero-3-3-mer

Ligands

6 x PXQ: 3-[5-[[(3~{R},4~{R})-3-ethyl-4-methyl-5-oxidanylidene-3,4-dihydropyrrol-2-yl]methyl]-2-[[5-[(~{Z})-(4-ethyl-3-methyl-5-oxidanylidene-pyrrol-2-ylidene)methyl]-3-(3-hydroxy-3-oxopropyl)-4-methyl-1~{H}-pyrrol-2-yl]methyl]-4-methyl-1~{H}-pyrrol-3-yl]propanoic acid(Covalent)(Non-covalent)

PXQ.1: 27 residues within 4Å: Chain A: L.57, V.64, N.70, A.71, M.76, T.79, C.80, R.82, D.83, L.84, Y.86, Y.87, I.106, M.114, Y.115, L.118, T.120, P.121, A.124, V.125 Chain F: L.61, Y.62, T.66, Y.73, T.74, T.75, Y.78 23 PLIP interactions: 15 interactions with chain A, 8 interactions with chain F Hydrophobic interactions: A:L.57, A:T.79, A:L.84, A:Y.86, A:Y.87, A:T.120, A:A.124, F:L.61, F:Y.62, F:Y.73, F:Y.78 Hydrogen bonds: A:R.82, A:D.83, A:D.83, F:Y.62, F:T.74 Water bridges: A:N.70, A:R.82, A:R.82, F:T.66, F:T.66 Salt bridges: A:R.82 pi-Cation interactions: A:R.82 PXQ.17: 22 residues within 4Å: Chain B: I.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, L.112, Y.116, L.119, V.121, P.122, A.125, T.126 Ligands: MPD.20 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:R.77, B:A.80, B:L.85, B:Y.87, B:Y.88, B:Y.91, B:L.112, B:L.112, B:L.119, B:V.121, B:V.121, B:A.125 Hydrogen bonds: B:R.83, B:D.84, B:D.84 Water bridges: B:R.76, B:Y.87 Salt bridges: B:R.76, B:R.83 pi-Cation interactions: B:R.83 PXQ.35: 27 residues within 4Å: Chain B: L.61, Y.62, T.66, Y.73, T.74, T.75, Y.78 Chain C: L.57, V.64, N.70, A.71, M.76, T.79, C.80, R.82, D.83, L.84, Y.86, Y.87, I.106, M.114, Y.115, L.118, T.120, P.121, A.124, V.125 22 PLIP interactions: 16 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:L.57, C:T.79, C:L.84, C:Y.86, C:Y.87, C:I.106, C:L.118, C:A.124, C:V.125, B:Y.62, B:Y.73, B:Y.78 Hydrogen bonds: C:A.71, C:R.82, C:D.83, C:D.83, B:Y.62, B:T.74 Water bridges: C:R.82, B:T.66 Salt bridges: C:R.82 pi-Cation interactions: C:R.82 PXQ.46: 24 residues within 4Å: Chain D: I.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, L.112, T.115, Y.116, L.119, V.121, P.122, A.125, T.126 Ligands: MPD.49, PEG.55 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:I.65, D:R.77, D:A.80, D:L.85, D:Y.87, D:Y.87, D:Y.88, D:Y.91, D:T.115, D:V.121, D:V.121, D:A.125 Hydrogen bonds: D:R.83, D:D.84, D:D.84 Water bridges: D:R.76, D:R.83 Salt bridges: D:R.76, D:R.83 pi-Cation interactions: D:R.83 PXQ.64: 27 residues within 4Å: Chain D: L.61, Y.62, T.66, Y.73, T.74, T.75, Y.78 Chain E: L.57, V.64, N.70, A.71, M.76, T.79, C.80, R.82, D.83, L.84, Y.86, Y.87, I.106, M.114, Y.115, L.118, T.120, P.121, A.124, V.125 22 PLIP interactions: 14 interactions with chain E, 8 interactions with chain D Hydrophobic interactions: E:L.57, E:T.79, E:L.84, E:Y.87, E:I.106, E:T.120, E:A.124, D:Y.62, D:Y.73, D:Y.78 Hydrogen bonds: E:R.82, E:D.83, E:D.83, D:Y.62, D:Y.62, D:T.66, D:T.74 Water bridges: E:R.82, D:T.66 Salt bridges: E:R.82 pi-Stacking: E:Y.86 pi-Cation interactions: E:R.82 PXQ.82: 22 residues within 4Å: Chain F: I.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, L.112, Y.116, L.119, V.121, P.122, A.125, T.126 Ligands: MPD.85 21 PLIP interactions: 21 interactions with chain F Hydrophobic interactions: F:R.77, F:A.80, F:L.85, F:Y.87, F:Y.88, F:Y.91, F:L.119, F:V.121, F:V.121, F:A.125 Hydrogen bonds: F:R.83, F:D.84, F:D.84 Water bridges: F:R.76, F:R.76, F:R.76, F:R.77 Salt bridges: F:R.76, F:R.77, F:R.83 pi-Cation interactions: F:R.83

12 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.2: 5 residues within 4Å: Chain A: Q.56, K.60, G.127, A.130, A.131 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:A.130 Hydrogen bonds: A:Q.56, A:G.127 MPD.18: 6 residues within 4Å: Chain B: T.33, L.36, R.37, D.144, A.145, E.148 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:T.33, B:A.145, B:E.148 Water bridges: B:D.144, B:D.144, B:A.145, B:E.148 MPD.19: 3 residues within 4Å: Chain B: E.54, V.136, L.140 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.54, B:V.136, B:L.140 MPD.20: 6 residues within 4Å: Chain B: E.106, R.107, V.108, N.110, T.115 Ligands: PXQ.17 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.108, B:N.110 MPD.36: 7 residues within 4Å: Chain C: D.63, V.64, G.68, G.69, N.70, G.119, P.121 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:N.70 Hydrogen bonds: C:D.63, C:D.63, C:N.70 MPD.47: 7 residues within 4Å: Chain D: T.33, L.36, R.37, R.39, D.144, A.145, E.148 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:T.33, D:R.37, D:D.144, D:E.148 Hydrogen bonds: D:R.39 MPD.48: 5 residues within 4Å: Chain D: A.50, V.136, L.140 Ligands: EDO.57, EDO.59 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:V.136 MPD.49: 7 residues within 4Å: Chain D: R.107, V.108, N.110, G.111, L.112, T.115 Ligands: PXQ.46 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.112 Hydrogen bonds: D:T.115 MPD.83: 6 residues within 4Å: Chain F: T.33, L.36, R.37, D.144, A.145, E.148 6 PLIP interactions: 6 interactions with chain F Hydrophobic interactions: F:T.33, F:R.37, F:A.145, F:E.148 Water bridges: F:A.145, F:E.148 MPD.84: 5 residues within 4Å: Chain F: N.47, A.50, V.136, L.140 Ligands: PGE.91 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:A.50, F:V.136, F:L.140 MPD.85: 5 residues within 4Å: Chain F: R.107, V.108, N.110, T.115 Ligands: PXQ.82 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:N.110 MPD.86: 6 residues within 4Å: Chain F: K.134, A.138, P.143, G.146, K.147 Ligands: PEG.93 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:K.134, F:P.143

2 x BCN: BICINE(Non-covalent)

BCN.3: 4 residues within 4Å: Chain A: F.58, P.62, V.65, S.66 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.58 BCN.50: 5 residues within 4Å: Chain B: R.77 Chain C: I.106 Chain D: N.10, D.13 Ligands: EDO.62 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Water bridges: B:R.77, B:R.77 Salt bridges: B:R.77, D:D.13 Hydrogen bonds: D:D.13

5 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.4: 3 residues within 4Å: Chain A: Q.59, K.60 Ligands: PEG.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.60 1PE.21: 2 residues within 4Å: Chain B: R.39 Ligands: EDO.28 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.39, B:R.39 1PE.22: 8 residues within 4Å: Chain A: A.33, L.36, R.37, Q.40 Chain B: N.21, L.24, E.25, K.28 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.25, B:E.25, B:E.25, B:K.28 1PE.33: 4 residues within 4Å: Chain B: V.14 Chain F: G.69 Ligands: EDO.31, PEG.94 No protein-ligand interaction detected (PLIP) 1PE.87: 6 residues within 4Å: Chain F: G.99, D.100, P.101, V.151, Y.152, Y.155 1 PLIP interactions: 1 interactions with chain F Water bridges: F:Q.2

11 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.5: 4 residues within 4Å: Chain A: N.9, A.12, E.13, R.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.9, A:R.15 PGE.15: 6 residues within 4Å: Chain A: R.24, S.27, F.28, R.35, E.143 Ligands: EDO.10 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.27, A:F.28, A:E.143 PGE.23: 6 residues within 4Å: Chain A: Y.16 Chain B: S.45, A.48, A.49, D.86 Chain C: K.116 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Water bridges: C:K.116, C:K.116, B:S.45, B:A.49 Hydrogen bonds: B:S.45 PGE.24: 6 residues within 4Å: Chain B: K.58, S.59, V.127, Q.128, Q.131, A.132 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.59, B:Q.128 Water bridges: B:G.124 PGE.37: 2 residues within 4Å: Chain C: Y.72, G.73 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:E.75 PGE.67: 3 residues within 4Å: Chain E: P.62, P.67 Ligands: PEG.70 1 PLIP interactions: 1 interactions with chain E Water bridges: E:P.62 PGE.81: 8 residues within 4Å: Chain E: R.37, Q.40, V.41 Chain F: N.21, L.24, E.25, K.28 Ligands: EDO.72 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:E.25, F:K.28 PGE.88: 5 residues within 4Å: Chain F: S.7, V.8, S.11, A.22, K.26 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:S.7, F:K.26 Water bridges: F:S.7 PGE.89: 5 residues within 4Å: Chain F: D.64, I.65, G.69, G.70 Ligands: PEG.95 1 PLIP interactions: 1 interactions with chain F Water bridges: F:P.68 PGE.90: 3 residues within 4Å: Chain F: E.54, K.58 Ligands: PGE.91 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:E.54 PGE.91: 3 residues within 4Å: Chain F: S.139 Ligands: MPD.84, PGE.90 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:S.139, F:S.139

23 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 3 residues within 4Å: Chain A: G.98, V.100, Y.151 Ligand excluded by PLIP PEG.7: 4 residues within 4Å: Chain A: E.75, A.78, T.79, R.82 Ligand excluded by PLIP PEG.8: 6 residues within 4Å: Chain A: T.4, K.5, V.8, T.101, E.105 Chain B: M.1 Ligand excluded by PLIP PEG.9: 2 residues within 4Å: Chain A: K.60 Ligands: 1PE.4 Ligand excluded by PLIP PEG.25: 4 residues within 4Å: Chain B: K.53, E.54, A.57, K.58 Ligand excluded by PLIP PEG.26: 4 residues within 4Å: Chain B: S.139, L.140, G.142 Ligands: EDO.28 Ligand excluded by PLIP PEG.27: 4 residues within 4Å: Chain B: D.154, C.157, S.158, S.161 Ligand excluded by PLIP PEG.38: 4 residues within 4Å: Chain C: V.50, A.78, R.82 Ligands: PEG.39 Ligand excluded by PLIP PEG.39: 4 residues within 4Å: Chain B: Y.62 Chain C: T.79 Ligands: EDO.32, PEG.38 Ligand excluded by PLIP PEG.40: 4 residues within 4Å: Chain C: A.137, G.138, L.140 Ligands: EDO.42 Ligand excluded by PLIP PEG.41: 4 residues within 4Å: Chain C: G.98, V.100, A.150, Y.151 Ligand excluded by PLIP PEG.44: 6 residues within 4Å: Chain C: T.43, D.44, R.46 Chain D: Y.18, L.19, D.20 Ligand excluded by PLIP PEG.54: 1 residues within 4Å: Chain D: R.39 Ligand excluded by PLIP PEG.55: 3 residues within 4Å: Chain D: R.76, A.80 Ligands: PXQ.46 Ligand excluded by PLIP PEG.56: 6 residues within 4Å: Chain D: K.58, S.59, Q.128, Q.131, A.132, E.135 Ligand excluded by PLIP PEG.68: 2 residues within 4Å: Chain E: Q.59, K.60 Ligand excluded by PLIP PEG.69: 2 residues within 4Å: Chain E: Q.59, K.60 Ligand excluded by PLIP PEG.70: 5 residues within 4Å: Chain E: V.65, S.66, Y.72 Ligands: PG4.66, PGE.67 Ligand excluded by PLIP PEG.71: 3 residues within 4Å: Chain E: Y.72, G.73 Ligands: PG4.66 Ligand excluded by PLIP PEG.92: 4 residues within 4Å: Chain F: M.1, Q.2, S.102, E.106 Ligand excluded by PLIP PEG.93: 7 residues within 4Å: Chain F: Q.131, K.134, K.147, G.150, V.151, D.154 Ligands: MPD.86 Ligand excluded by PLIP PEG.94: 8 residues within 4Å: Chain B: V.14 Chain F: G.69, G.70, N.71, R.77, G.120 Ligands: 1PE.33, PEG.95 Ligand excluded by PLIP PEG.95: 4 residues within 4Å: Chain F: G.120, P.122 Ligands: PGE.89, PEG.94 Ligand excluded by PLIP

34 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.10: 3 residues within 4Å: Chain A: G.146, E.147 Ligands: PGE.15 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: L.139, L.140, S.141, D.144 Ligand excluded by PLIP EDO.12: 3 residues within 4Å: Chain A: D.123, G.127, Q.160 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: K.5, V.100, T.101, E.104 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain A: D.11 Chain B: Y.91, R.107 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: Q.34, R.35, I.38, E.143, D.144, E.147 Ligand excluded by PLIP EDO.28: 4 residues within 4Å: Chain B: G.142, P.143 Ligands: 1PE.21, PEG.26 Ligand excluded by PLIP EDO.29: 4 residues within 4Å: Chain B: K.58, E.135, V.136, S.139 Ligand excluded by PLIP EDO.30: 1 residues within 4Å: Chain B: S.118 Ligand excluded by PLIP EDO.31: 4 residues within 4Å: Chain B: Q.2, S.7, S.11 Ligands: 1PE.33 Ligand excluded by PLIP EDO.32: 2 residues within 4Å: Chain B: Y.62 Ligands: PEG.39 Ligand excluded by PLIP EDO.34: 1 residues within 4Å: Chain C: E.113 Ligand excluded by PLIP EDO.42: 1 residues within 4Å: Ligands: PEG.40 Ligand excluded by PLIP EDO.43: 4 residues within 4Å: Chain C: S.27, F.28, G.31, R.35 Ligand excluded by PLIP EDO.45: 2 residues within 4Å: Chain C: E.105 Chain D: M.1 Ligand excluded by PLIP EDO.57: 4 residues within 4Å: Chain D: A.46, N.47, A.50 Ligands: MPD.48 Ligand excluded by PLIP EDO.58: 4 residues within 4Å: Chain D: K.134, P.143, G.146, K.147 Ligand excluded by PLIP EDO.59: 4 residues within 4Å: Chain D: E.54, K.58, S.139 Ligands: MPD.48 Ligand excluded by PLIP EDO.60: 4 residues within 4Å: Chain D: G.69, N.71, R.77 Chain F: V.14 Ligand excluded by PLIP EDO.61: 3 residues within 4Å: Chain D: V.127, C.157, S.161 Ligand excluded by PLIP EDO.62: 3 residues within 4Å: Chain C: E.105 Chain D: N.10 Ligands: BCN.50 Ligand excluded by PLIP EDO.72: 3 residues within 4Å: Chain E: Q.34, R.37 Ligands: PGE.81 Ligand excluded by PLIP EDO.73: 3 residues within 4Å: Chain E: D.55, Q.56, Q.59 Ligand excluded by PLIP EDO.74: 2 residues within 4Å: Chain E: G.31, R.35 Ligand excluded by PLIP EDO.75: 5 residues within 4Å: Chain E: K.116, G.119, T.120 Ligands: EDO.76, EDO.79 Ligand excluded by PLIP EDO.76: 7 residues within 4Å: Chain E: Y.115, K.116, T.120, P.121, I.122 Ligands: EDO.75, EDO.79 Ligand excluded by PLIP EDO.77: 2 residues within 4Å: Chain E: D.153, Y.154 Ligand excluded by PLIP EDO.78: 3 residues within 4Å: Chain E: Q.56, G.127, A.131 Ligand excluded by PLIP EDO.79: 3 residues within 4Å: Chain E: K.116 Ligands: EDO.75, EDO.76 Ligand excluded by PLIP EDO.80: 3 residues within 4Å: Chain E: D.123, A.126, G.127 Ligand excluded by PLIP EDO.96: 4 residues within 4Å: Chain E: A.14, Y.16 Chain F: Y.87, R.90 Ligand excluded by PLIP EDO.97: 2 residues within 4Å: Chain F: Y.62, R.67 Ligand excluded by PLIP EDO.98: 4 residues within 4Å: Chain F: D.105, L.109, N.110, G.159 Ligand excluded by PLIP EDO.99: 5 residues within 4Å: Chain D: Y.73 Chain E: I.106 Chain F: N.10, D.13, V.14 Ligand excluded by PLIP

5 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.51: 5 residues within 4Å: Chain C: L.36, Q.40 Chain D: L.24, E.25, K.28 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:E.25, D:K.28, C:Q.40 PG4.52: 8 residues within 4Å: Chain D: A.57, K.58, S.59, L.60, L.61, S.63, A.125, Q.128 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:A.57 Water bridges: D:A.125 PG4.53: 5 residues within 4Å: Chain D: P.101, K.147, E.148, V.151, Y.152 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.147 PG4.63: 4 residues within 4Å: Chain D: A.48, A.49, D.86 Chain E: K.116 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.116 PG4.66: 9 residues within 4Å: Chain E: F.58, Q.59, V.65, A.71, Y.72, G.73, T.77 Ligands: PEG.70, PEG.71 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:V.65, E:G.73 Water bridges: E:Q.59

1 x MRD: (4R)-2-METHYLPENTANE-2,4-DIOL(Non-functional Binders)

MRD.65: 3 residues within 4Å: Chain E: R.46, E.47, D.85 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:R.46 Hydrogen bonds: E:E.47

Links

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Citation

Patel, H.M. et al., The high resolution structure of allophycocyanin from cyanobacterium Nostoc sp. WR13. To Be Published

Release Date

2021-05-12

Peptides

ALPHA SUBUNIT OF CYANOBACTERIAL ALLOPHYCOCYANIN PROTEIN: ACE
BETA SUBUNIT OF CYANOBACTERIAL ALLOPHYCOCYANIN PROTEIN: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

C
CCC

E
EEE

B
BBB

D
DDD

F
FFF

ALPHA SUBUNIT OF CYANOBACTERIAL ALLOPHYCOCYANIN PROTEIN

BETA SUBUNIT OF CYANOBACTERIAL ALLOPHYCOCYANIN PROTEIN

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