SMTL ID : 6yx7.1

The high resolution structure of allophycocyanin from cyanobacterium Nostoc sp. WR13, the P21212 crystal form.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 Å

Oligo State

hetero-6-6-mer

Ligands

12 x CYC: PHYCOCYANOBILIN(Covalent)

CYC.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 25 PLIP interactions: 14 interactions with chain A, 11 interactions with chain F Hydrophobic interactions: A:L.57, A:T.79, A:L.84, A:Y.87, A:L.118, A:A.124, F:L.61, F:Y.62, F:Y.73, F:T.75, F:Y.78 Hydrogen bonds: A:N.70, A:R.82, A:D.83, F:Y.62, F:Y.62, F:T.66, F:T.74 Water bridges: A:R.82, A:Y.86, F:T.66, F:T.66 Salt bridges: A:R.82 pi-Stacking: A:Y.86 pi-Cation interactions: A:R.82 CYC.3: 24 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, T.115, Y.116, L.119, V.121, P.122, A.125, T.126 Ligands: PG4.2, LYS.4 25 PLIP interactions: 22 interactions with chain B, 3 Ligand-Ligand interactions Hydrophobic interactions: B:I.65, B:R.77, B:A.80, B:L.85, B:Y.87, B:Y.87, B:Y.88, B:Y.91, B:T.115, B:L.119, B:V.121, B:V.121, B:A.125, K.4 Hydrogen bonds: B:R.83, B:D.84, K.4, K.4 Water bridges: B:R.76, B:R.76, B:R.76, B:R.76 Salt bridges: B:R.76, B:R.77, B:R.83 CYC.11: 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 26 PLIP interactions: 11 interactions with chain B, 15 interactions with chain C Hydrophobic interactions: B:L.61, B:Y.62, B:Y.73, B:T.75, B:Y.78, C:L.57, C:T.79, C:L.84, C:Y.87, C:L.118, C:A.124 Hydrogen bonds: B:Y.62, B:Y.62, B:Y.62, B:T.66, B:T.74, C:N.70, C:R.82, C:D.83 Water bridges: B:T.66, C:N.70, C:R.82, C:R.82 Salt bridges: C:R.82 pi-Stacking: C:Y.86 pi-Cation interactions: C:R.82 CYC.17: 23 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: GLU.18 26 PLIP interactions: 24 interactions with chain D, 2 Ligand-Ligand interactions Hydrophobic interactions: D:R.77, D:A.80, D:L.85, D:Y.87, D:Y.87, D:Y.87, D:Y.88, D:Y.91, D:T.115, D:L.119, D:V.121, D:V.121, D:A.125 Hydrogen bonds: D:R.83, D:D.84, E.18 Water bridges: D:R.76, D:R.76, D:R.76, D:R.83, D:Y.87, E.18 Salt bridges: D:R.76, D:R.77, D:R.83 pi-Cation interactions: D:R.83 CYC.20: 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 27 PLIP interactions: 11 interactions with chain D, 16 interactions with chain E Hydrophobic interactions: D:L.61, D:Y.62, D:Y.73, D:T.75, D:Y.78, E:L.57, E:T.79, E:L.84, E:Y.87, E:I.106, E:T.120, E:A.124 Hydrogen bonds: D:Y.62, D:Y.62, D:T.66, D:T.74, E:N.70, E:R.82, E:D.83 Water bridges: D:T.66, D:T.66, E:N.70, E:R.82, E:R.82, E:Y.86 Salt bridges: E:R.82 pi-Stacking: E:Y.86 CYC.23: 23 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, T.115, Y.116, L.119, V.121, P.122, A.125, T.126 Ligands: ALA.24 22 PLIP interactions: 21 interactions with chain F, 1 Ligand-Ligand interactions Hydrophobic interactions: F:R.77, F:A.80, F:L.85, F:Y.87, F:Y.87, F:Y.88, F:Y.91, F:T.115, F:L.119, F:V.121, F:V.121, F:A.125, A.24 Hydrogen bonds: F:R.83, 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 CYC.27: 27 residues within 4Å: Chain G: 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 L: L.61, Y.62, T.66, Y.73, T.74, T.75, Y.78 23 PLIP interactions: 14 interactions with chain G, 9 interactions with chain L Hydrophobic interactions: G:L.57, G:T.79, G:L.84, G:Y.86, G:Y.87, G:I.106, G:A.124, L:L.61, L:Y.62, L:Y.73, L:T.75, L:Y.78 Hydrogen bonds: G:N.70, G:R.82, G:D.83, L:Y.62, L:Y.62, L:T.74 Water bridges: G:N.70, G:R.82, L:T.66 Salt bridges: G:R.82 pi-Cation interactions: G:R.82 CYC.32: 23 residues within 4Å: Chain H: 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: GLU.33 24 PLIP interactions: 23 interactions with chain H, 1 Ligand-Ligand interactions Hydrophobic interactions: H:R.77, H:A.80, H:L.85, H:Y.87, H:Y.87, H:Y.88, H:Y.91, H:T.115, H:L.119, H:V.121, H:V.121, H:A.125 Hydrogen bonds: H:R.83, H:D.84, E.33 Water bridges: H:R.76, H:R.76, H:R.76, H:R.76, H:R.83, H:Y.87 Salt bridges: H:R.76, H:R.77, H:R.83 CYC.36: 27 residues within 4Å: Chain H: L.61, Y.62, T.66, Y.73, T.74, T.75, Y.78 Chain I: 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 27 PLIP interactions: 12 interactions with chain H, 15 interactions with chain I Hydrophobic interactions: H:L.61, H:Y.62, H:Y.73, H:T.75, H:Y.78, I:L.57, I:T.79, I:L.84, I:Y.87, I:I.106, I:T.120, I:A.124 Hydrogen bonds: H:Y.62, H:Y.62, H:Y.62, H:T.74, I:N.70, I:R.82, I:D.83 Water bridges: H:T.66, H:T.66, H:T.66, I:N.70, I:R.82 Salt bridges: I:R.82 pi-Stacking: I:Y.86 pi-Cation interactions: I:R.82 CYC.38: 23 residues within 4Å: Chain J: 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: DSN.39 22 PLIP interactions: 22 interactions with chain J Hydrophobic interactions: J:R.77, J:A.80, J:L.85, J:Y.87, J:Y.87, J:Y.88, J:Y.91, J:L.112, J:T.115, J:L.119, J:V.121, J:V.121, J:A.125 Hydrogen bonds: J:R.83, J:D.84 Water bridges: J:R.76, J:R.76, J:R.76, J:R.76 Salt bridges: J:R.76, J:R.77, J:R.83 CYC.43: 27 residues within 4Å: Chain J: L.61, Y.62, T.66, Y.73, T.74, T.75, Y.78 Chain K: 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 25 PLIP interactions: 15 interactions with chain K, 10 interactions with chain J Hydrophobic interactions: K:L.57, K:T.79, K:L.84, K:Y.87, K:T.120, K:A.124, J:L.61, J:Y.62, J:Y.73, J:T.75, J:Y.78 Hydrogen bonds: K:N.70, K:R.82, K:D.83, J:Y.62, J:Y.62, J:Y.62, J:T.74 Water bridges: K:N.70, K:R.82, K:R.82, J:T.66 Salt bridges: K:R.82 pi-Stacking: K:Y.86 pi-Cation interactions: K:R.82 CYC.47: 23 residues within 4Å: Chain L: 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: DSN.48 22 PLIP interactions: 22 interactions with chain L Hydrophobic interactions: L:I.65, L:R.77, L:A.80, L:L.85, L:Y.87, L:Y.87, L:Y.88, L:Y.91, L:T.115, L:L.119, L:V.121, L:V.121, L:P.122, L:A.125 Hydrogen bonds: L:R.83, L:D.84 Water bridges: L:R.76, L:R.76, L:R.76 Salt bridges: L:R.76, L:R.77, L:R.83

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

PG4.2: 8 residues within 4Å: Chain A: D.11, A.14 Chain B: Y.87, R.90, Y.91, R.107 Ligands: CYC.3, LYS.4 6 PLIP interactions: 2 Ligand-Ligand interactions, 4 interactions with chain B Hydrogen bonds: K.4, K.4, B:R.90, B:R.90, B:Y.91, B:R.107 PG4.13: 4 residues within 4Å: Chain C: R.48, G.138, L.139 Ligands: P6G.12 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:R.48, C:R.48 Water bridges: C:N.45 PG4.26: 2 residues within 4Å: Chain F: R.39, V.141 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.39 Water bridges: F:R.39 PG4.41: 2 residues within 4Å: Chain J: L.36, R.39 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:R.39, J:R.39

3 x LYS: LYSINE(Non-covalent)

LYS.4: 6 residues within 4Å: Chain B: V.108, N.110, G.111, T.115 Ligands: PG4.2, CYC.3 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.115, B:T.115 Water bridges: B:Y.87, B:N.110 LYS.37: 5 residues within 4Å: Chain E: N.9, E.13 Chain I: K.5, N.9, E.13 5 PLIP interactions: 3 interactions with chain E, 2 interactions with chain I Hydrogen bonds: E:N.9, E:E.13, I:N.9, I:E.13 Water bridges: E:R.15 LYS.44: 4 residues within 4Å: Chain J: Y.62 Chain K: E.75, A.78, T.79 6 PLIP interactions: 5 interactions with chain K, 1 interactions with chain J, Hydrophobic interactions: K:E.75, J:Y.62 Hydrogen bonds: K:T.79 Water bridges: K:A.78, K:T.79, K:T.79

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

MPD.5: 6 residues within 4Å: Chain B: T.33, L.36, R.37, D.144, A.145, E.148 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:T.33, B:A.145, B:E.148 Water bridges: B:A.145, B:E.148 MPD.19: 6 residues within 4Å: Chain D: T.33, L.36, R.37, D.144, A.145, E.148 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:L.36, D:R.37, D:A.145 Water bridges: D:E.148, D:E.148, D:E.148 MPD.22: 4 residues within 4Å: Chain E: V.100, A.150, Y.151 Chain I: P.19 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:A.150, E:Y.151 MPD.25: 6 residues within 4Å: Chain F: T.33, L.36, R.37, D.144, A.145, E.148 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:T.33, F:A.145, F:E.148 Water bridges: F:A.145 MPD.34: 6 residues within 4Å: Chain H: T.33, L.36, R.37, D.144, A.145, E.148 5 PLIP interactions: 5 interactions with chain H Hydrophobic interactions: H:L.36, H:R.37, H:A.145 Water bridges: H:E.148, H:E.148 MPD.40: 6 residues within 4Å: Chain J: T.33, L.36, R.37, D.144, A.145, E.148 4 PLIP interactions: 4 interactions with chain J Hydrophobic interactions: J:T.33, J:A.145, J:E.148 Water bridges: J:A.145 MPD.49: 6 residues within 4Å: Chain L: T.33, L.36, R.37, D.144, A.145, E.148 7 PLIP interactions: 7 interactions with chain L Hydrophobic interactions: L:T.33, L:A.145, L:E.148 Water bridges: L:D.144, L:D.144, L:A.145, L:E.148

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

1PE.6: 9 residues within 4Å: Chain B: R.39, A.138, S.139, L.140, V.141, G.142, P.143 Ligands: PEG.7, PEG.8 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.39, B:G.142

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

PEG.7: 6 residues within 4Å: Chain B: L.36, R.39, D.144 Ligands: 1PE.6, PEG.8, PGE.30 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.39, B:R.39 Water bridges: B:D.144, B:A.145 PEG.8: 4 residues within 4Å: Chain B: P.143, D.144 Ligands: 1PE.6, PEG.7 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.144 PEG.10: 7 residues within 4Å: Chain G: K.133, A.145, G.146, G.149, A.150, D.153 Ligands: PGE.29 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain G Water bridges: A:K.26, G:K.133, G:K.133, G:D.153 Hydrogen bonds: G:K.133 PEG.14: 5 residues within 4Å: Chain C: D.23, R.24, S.27, F.28 Chain K: S.27 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.23, C:S.27, C:F.28 Water bridges: C:R.24 PEG.31: 3 residues within 4Å: Chain G: D.55, Q.56, Q.59 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:D.55 Water bridges: G:Q.56, G:Q.59 PEG.35: 6 residues within 4Å: Chain H: S.7, V.8, S.11, A.22, A.23, K.26 6 PLIP interactions: 6 interactions with chain H Hydrogen bonds: H:S.7, H:S.11, H:A.22 Water bridges: H:S.7, H:S.7, H:A.23 PEG.42: 4 residues within 4Å: Chain J: S.59, S.63, I.65, Q.128 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:S.63, J:Q.128 Water bridges: J:D.64

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

EDO.9: 5 residues within 4Å: Chain B: N.47 Chain G: A.126, G.127, A.130, V.156 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain B Water bridges: G:G.127, G:K.133, G:K.133 Hydrogen bonds: B:N.47, B:N.47 EDO.15: 3 residues within 4Å: Chain C: Q.74, E.75, A.78 No protein-ligand interaction detected (PLIP) EDO.16: 6 residues within 4Å: Chain C: R.61, D.63, P.121 Chain G: R.61, D.63, P.121 8 PLIP interactions: 4 interactions with chain C, 4 interactions with chain G Hydrogen bonds: C:R.61, G:R.61 Water bridges: C:R.61, C:G.119, C:D.123, G:R.61, G:D.63, G:G.119 EDO.45: 4 residues within 4Å: Chain K: V.65, G.73, Q.74, T.77 1 PLIP interactions: 1 interactions with chain K Water bridges: K:G.73 EDO.46: 6 residues within 4Å: Chain E: K.60 Chain K: D.63, S.66, P.67, G.68, G.69 4 PLIP interactions: 1 interactions with chain E, 3 interactions with chain K Water bridges: E:R.61, K:S.66 Hydrogen bonds: K:S.66, K:S.66

1 x P6G: HEXAETHYLENE GLYCOL(Non-functional Binders)

P6G.12: 5 residues within 4Å: Chain C: G.138, L.139, L.140, S.141 Ligands: PG4.13 No protein-ligand interaction detected (PLIP)

2 x GLU: GLUTAMIC ACID(Non-covalent)

GLU.18: 7 residues within 4Å: Chain D: E.106, R.107, V.108, N.110, L.112, T.115 Ligands: CYC.17 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:V.108, D:V.108, D:N.110, D:T.115 GLU.33: 7 residues within 4Å: Chain H: E.106, R.107, N.110, G.111, L.112, T.115 Ligands: CYC.32 7 PLIP interactions: 1 interactions with chain H, 6 Ligand-Ligand interactions Water bridges: H:N.110 Hydrogen bonds: E.33, E.33, E.33, E.33, E.33, E.33

1 x GLY: GLYCINE(Non-covalent)

GLY.21: 4 residues within 4Å: Chain E: Q.34, R.35, D.144, E.147 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:Q.34, E:D.144 Water bridges: E:R.35, E:R.35 Salt bridges: E:R.35

1 x ALA: ALANINE(Non-covalent)

ALA.24: 4 residues within 4Å: Chain F: R.107, V.108, N.110 Ligands: CYC.23 4 PLIP interactions: 1 Ligand-Ligand interactions, 3 interactions with chain F Hydrogen bonds: A.24, F:N.110, F:N.110, F:N.110

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

MRD.28: 3 residues within 4Å: Chain G: R.46, E.47, D.85 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:R.46 Water bridges: G:E.47

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

PGE.29: 9 residues within 4Å: Chain G: K.133, S.134, A.136, A.137, A.145, A.148, G.149, F.152 Ligands: PEG.10 3 PLIP interactions: 3 interactions with chain G Water bridges: G:K.133, G:S.134, G:S.134 PGE.30: 3 residues within 4Å: Chain G: A.142, E.143 Ligands: PEG.7 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:A.142, G:E.143 PGE.50: 4 residues within 4Å: Chain L: S.139, V.141, G.142, P.143 No protein-ligand interaction detected (PLIP)

2 x DSN: D-SERINE(Non-covalent)

DSN.39: 4 residues within 4Å: Chain J: V.108, N.110, T.115 Ligands: CYC.38 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:N.110 Water bridges: J:N.110 DSN.48: 7 residues within 4Å: Chain L: R.107, V.108, N.110, G.111, L.112, T.115 Ligands: CYC.47 2 PLIP interactions: 2 interactions with chain L Hydrogen bonds: L:G.111 Water bridges: L:N.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

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

Allophycocyanin alpha: ACEGIK
Allophycocyanin beta: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

C
CCC

E
EEE

G
GGG

I
III

K
KKK

B
BBB

D
DDD

F
FFF

H
HHH

J
JJJ

L
LLL

Allophycocyanin alpha

Allophycocyanin beta

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