SMTL ID : 1eyx.2 (1 other biounit)

CRYSTAL STRUCTURE OF R-PHYCOERYTHRIN AT 2.2 ANGSTROMS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

hetero-6-6-mer

Ligands

6 x ALA- ALA- PHE- ARG- ALA- ALA: R-PHYCOERYTHRIN(Non-covalent)

ALA-ALA-PHE-ARG-ALA-ALA.1: 8 residues within 4Å: Chain B: C.109, N.111, G.112, L.113, E.115, T.116, A.119 Ligands: CYC.8 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.113, B:T.116, B:A.119 ALA-ALA-PHE-ARG-ALA-ALA.2: 8 residues within 4Å: Chain D: C.109, N.111, G.112, L.113, E.115, T.116, A.119 Ligands: CYC.13 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.113, D:T.116, D:A.119 Hydrogen bonds: D:T.116 ALA-ALA-PHE-ARG-ALA-ALA.15: 8 residues within 4Å: Chain F: C.109, N.111, G.112, L.113, E.115, T.116, A.119 Ligands: CYC.22 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:L.113, F:T.116, F:A.119 ALA-ALA-PHE-ARG-ALA-ALA.16: 8 residues within 4Å: Chain H: C.109, N.111, G.112, L.113, E.115, T.116, A.119 Ligands: CYC.27 4 PLIP interactions: 4 interactions with chain H Hydrophobic interactions: H:L.113, H:T.116, H:A.119 Hydrogen bonds: H:T.116 ALA-ALA-PHE-ARG-ALA-ALA.29: 8 residues within 4Å: Chain J: C.109, N.111, G.112, L.113, E.115, T.116, A.119 Ligands: CYC.36 3 PLIP interactions: 3 interactions with chain J Hydrophobic interactions: J:L.113, J:T.116, J:A.119 ALA-ALA-PHE-ARG-ALA-ALA.30: 8 residues within 4Å: Chain L: C.109, N.111, G.112, L.113, E.115, T.116, A.119 Ligands: CYC.41 4 PLIP interactions: 4 interactions with chain L Hydrophobic interactions: L:L.113, L:T.116, L:A.119 Hydrogen bonds: L:T.116

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: G.64, Y.65, N.68 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.68 Water bridges: A:G.64, A:N.68 SO4.6: 3 residues within 4Å: Chain B: G.100, E.164, Y.168 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.168 Water bridges: B:E.164 SO4.17: 3 residues within 4Å: Chain E: G.64, Y.65, N.68 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:N.68 Water bridges: E:G.64, E:N.68 SO4.20: 3 residues within 4Å: Chain F: G.100, E.164, Y.168 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:Y.168 Water bridges: F:E.164 SO4.31: 3 residues within 4Å: Chain I: G.64, Y.65, N.68 3 PLIP interactions: 3 interactions with chain I Hydrogen bonds: I:N.68 Water bridges: I:G.64, I:N.68 SO4.34: 3 residues within 4Å: Chain J: G.100, E.164, Y.168 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:Y.168 Water bridges: J:E.164

3 x BLA: BILIVERDINE IX ALPHA(Covalent)

BLA.4: 24 residues within 4Å: Chain A: C.59, F.60, A.72, G.73, K.78, K.81, C.82, R.84, D.85, H.88, Y.89, W.108, Y.117, L.120, L.122, P.123, A.126, Y.127 Chain J: S.57, I.67, Y.74, T.75, N.76, M.79 22 PLIP interactions: 17 interactions with chain A, 5 interactions with chain J Hydrophobic interactions: A:K.78, A:K.81, A:K.81, A:H.88, A:Y.89, A:L.120, J:I.67, J:Y.74, J:M.79 Hydrogen bonds: A:A.72, A:R.84, A:D.85, A:H.88, A:Y.127, J:S.57, J:T.75 Water bridges: A:E.71, A:K.78 Salt bridges: A:K.78, A:K.81, A:R.84 pi-Cation interactions: A:R.84 BLA.18: 24 residues within 4Å: Chain B: S.57, I.67, Y.74, T.75, N.76, M.79 Chain E: C.59, F.60, A.72, G.73, K.78, K.81, C.82, R.84, D.85, H.88, Y.89, W.108, Y.117, L.120, L.122, P.123, A.126, Y.127 22 PLIP interactions: 17 interactions with chain E, 5 interactions with chain B Hydrophobic interactions: E:K.78, E:K.81, E:K.81, E:H.88, E:Y.89, E:L.120, B:I.67, B:Y.74, B:M.79 Hydrogen bonds: E:A.72, E:R.84, E:D.85, E:H.88, E:Y.127, B:S.57, B:T.75 Water bridges: E:E.71, E:K.78 Salt bridges: E:K.78, E:K.81, E:R.84 pi-Cation interactions: E:R.84 BLA.32: 24 residues within 4Å: Chain F: S.57, I.67, Y.74, T.75, N.76, M.79 Chain I: C.59, F.60, A.72, G.73, K.78, K.81, C.82, R.84, D.85, H.88, Y.89, W.108, Y.117, L.120, L.122, P.123, A.126, Y.127 22 PLIP interactions: 17 interactions with chain I, 5 interactions with chain F Hydrophobic interactions: I:K.78, I:K.81, I:K.81, I:H.88, I:Y.89, I:L.120, F:I.67, F:Y.74, F:M.79 Hydrogen bonds: I:A.72, I:R.84, I:D.85, I:H.88, I:Y.127, F:S.57, F:T.75 Water bridges: I:E.71, I:K.78 Salt bridges: I:K.78, I:K.81, I:R.84 pi-Cation interactions: I:R.84

21 x CYC: PHYCOCYANOBILIN(Covalent)

CYC.5: 11 residues within 4Å: Chain A: K.43, L.44, N.47, V.51, E.54, R.137, L.138, C.139, R.142, D.143, Y.152 Ligand excluded by PLIP CYC.8: 20 residues within 4Å: Chain B: M.59, L.66, N.72, C.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, R.108, L.113, Y.117, L.120, V.122, P.123, S.126, T.127 Ligands: ALA-ALA-PHE-ARG-ALA-ALA.1 Ligand excluded by PLIP CYC.9: 20 residues within 4Å: Chain A: L.24, Q.28 Chain B: S.32, D.33, N.35, K.36, L.38, D.39, A.40, Y.43, I.142, S.143, N.144, V.153, I.154, E.155, G.156, C.158 Chain C: R.33, Q.147 Ligand excluded by PLIP CYC.10: 24 residues within 4Å: Chain C: C.59, F.60, A.72, G.73, K.78, K.81, C.82, R.84, D.85, H.88, Y.89, W.108, Y.117, L.120, L.122, P.123, A.126, Y.127 Chain H: S.57, I.67, Y.74, T.75, N.76, M.79 Ligand excluded by PLIP CYC.11: 12 residues within 4Å: Chain C: K.43, L.44, N.47, A.50, V.51, E.54, R.137, L.138, C.139, R.142, D.143, Y.152 Ligand excluded by PLIP CYC.13: 21 residues within 4Å: Chain D: M.59, L.66, N.72, C.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, R.108, C.109, L.113, Y.117, L.120, V.122, P.123, S.126, T.127 Ligands: ALA-PHE-ARG-ALA-ALA.2 Ligand excluded by PLIP CYC.14: 18 residues within 4Å: Chain A: R.33, Q.147 Chain C: L.24, Q.28 Chain D: S.32, N.35, K.36, L.38, D.39, Y.43, I.142, S.143, N.144, V.153, I.154, E.155, G.156, C.158 Ligand excluded by PLIP CYC.19: 11 residues within 4Å: Chain E: K.43, L.44, N.47, V.51, E.54, R.137, L.138, C.139, R.142, D.143, Y.152 Ligand excluded by PLIP CYC.22: 20 residues within 4Å: Chain F: M.59, L.66, N.72, C.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, R.108, L.113, Y.117, L.120, V.122, P.123, S.126, T.127 Ligands: ALA-ALA-PHE-ARG-ALA-ALA.15 Ligand excluded by PLIP CYC.23: 20 residues within 4Å: Chain E: L.24, Q.28 Chain F: S.32, D.33, N.35, K.36, L.38, D.39, A.40, Y.43, I.142, S.143, N.144, V.153, I.154, E.155, G.156, C.158 Chain G: R.33, Q.147 Ligand excluded by PLIP CYC.24: 24 residues within 4Å: Chain G: C.59, F.60, A.72, G.73, K.78, K.81, C.82, R.84, D.85, H.88, Y.89, W.108, Y.117, L.120, L.122, P.123, A.126, Y.127 Chain L: S.57, I.67, Y.74, T.75, N.76, M.79 Ligand excluded by PLIP CYC.25: 12 residues within 4Å: Chain G: K.43, L.44, N.47, A.50, V.51, E.54, R.137, L.138, C.139, R.142, D.143, Y.152 Ligand excluded by PLIP CYC.27: 21 residues within 4Å: Chain H: M.59, L.66, N.72, C.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, R.108, C.109, L.113, Y.117, L.120, V.122, P.123, S.126, T.127 Ligands: ALA-PHE-ARG-ALA-ALA.16 Ligand excluded by PLIP CYC.28: 18 residues within 4Å: Chain E: R.33, Q.147 Chain G: L.24, Q.28 Chain H: S.32, N.35, K.36, L.38, D.39, Y.43, I.142, S.143, N.144, V.153, I.154, E.155, G.156, C.158 Ligand excluded by PLIP CYC.33: 11 residues within 4Å: Chain I: K.43, L.44, N.47, V.51, E.54, R.137, L.138, C.139, R.142, D.143, Y.152 Ligand excluded by PLIP CYC.36: 20 residues within 4Å: Chain J: M.59, L.66, N.72, C.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, R.108, L.113, Y.117, L.120, V.122, P.123, S.126, T.127 Ligands: ALA-ALA-PHE-ARG-ALA-ALA.29 Ligand excluded by PLIP CYC.37: 20 residues within 4Å: Chain I: L.24, Q.28 Chain J: S.32, D.33, N.35, K.36, L.38, D.39, A.40, Y.43, I.142, S.143, N.144, V.153, I.154, E.155, G.156, C.158 Chain K: R.33, Q.147 Ligand excluded by PLIP CYC.38: 24 residues within 4Å: Chain D: S.57, I.67, Y.74, T.75, N.76, M.79 Chain K: C.59, F.60, A.72, G.73, K.78, K.81, C.82, R.84, D.85, H.88, Y.89, W.108, Y.117, L.120, L.122, P.123, A.126, Y.127 Ligand excluded by PLIP CYC.39: 12 residues within 4Å: Chain K: K.43, L.44, N.47, A.50, V.51, E.54, R.137, L.138, C.139, R.142, D.143, Y.152 Ligand excluded by PLIP CYC.41: 21 residues within 4Å: Chain L: M.59, L.66, N.72, C.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, R.108, C.109, L.113, Y.117, L.120, V.122, P.123, S.126, T.127 Ligands: ALA-PHE-ARG-ALA-ALA.30 Ligand excluded by PLIP CYC.42: 18 residues within 4Å: Chain I: R.33, Q.147 Chain K: L.24, Q.28 Chain L: S.32, N.35, K.36, L.38, D.39, Y.43, I.142, S.143, N.144, V.153, I.154, E.155, G.156, C.158 Ligand excluded by PLIP

6 x PUB: PHYCOUROBILIN(Covalent)

PUB.7: 15 residues within 4Å: Chain B: C.50, D.54, G.58, C.61, E.62, R.129, S.132, I.133, A.136, A.137, A.140, F.141, S.147, Q.148, R.149 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:D.54, B:I.133, B:I.133, B:A.136, B:A.137, B:F.141, B:Q.148 Hydrogen bonds: B:D.54, B:S.147, B:S.147, B:S.147, B:Q.148, B:R.149 Salt bridges: B:R.129 PUB.12: 17 residues within 4Å: Chain D: C.50, D.54, G.58, C.61, E.62, R.129, S.132, I.133, A.136, A.137, A.140, F.141, T.145, A.146, S.147, Q.148, R.149 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:D.54, D:I.133, D:I.133, D:A.136, D:A.137, D:A.140, D:Q.148 Hydrogen bonds: D:D.54, D:S.147, D:S.147, D:S.147, D:Q.148, D:R.149 Water bridges: D:A.136 Salt bridges: D:R.129 PUB.21: 15 residues within 4Å: Chain F: C.50, D.54, G.58, C.61, E.62, R.129, S.132, I.133, A.136, A.137, A.140, F.141, S.147, Q.148, R.149 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:D.54, F:I.133, F:I.133, F:A.136, F:A.137, F:F.141, F:Q.148 Hydrogen bonds: F:D.54, F:S.147, F:S.147, F:S.147, F:Q.148, F:R.149 Salt bridges: F:R.129 PUB.26: 17 residues within 4Å: Chain H: C.50, D.54, G.58, C.61, E.62, R.129, S.132, I.133, A.136, A.137, A.140, F.141, T.145, A.146, S.147, Q.148, R.149 15 PLIP interactions: 15 interactions with chain H Hydrophobic interactions: H:D.54, H:I.133, H:I.133, H:A.136, H:A.137, H:A.140, H:Q.148 Hydrogen bonds: H:D.54, H:S.147, H:S.147, H:S.147, H:Q.148, H:R.149 Water bridges: H:A.136 Salt bridges: H:R.129 PUB.35: 15 residues within 4Å: Chain J: C.50, D.54, G.58, C.61, E.62, R.129, S.132, I.133, A.136, A.137, A.140, F.141, S.147, Q.148, R.149 14 PLIP interactions: 14 interactions with chain J Hydrophobic interactions: J:D.54, J:I.133, J:I.133, J:A.136, J:A.137, J:F.141, J:Q.148 Hydrogen bonds: J:D.54, J:S.147, J:S.147, J:S.147, J:Q.148, J:R.149 Salt bridges: J:R.129 PUB.40: 17 residues within 4Å: Chain L: C.50, D.54, G.58, C.61, E.62, R.129, S.132, I.133, A.136, A.137, A.140, F.141, T.145, A.146, S.147, Q.148, R.149 15 PLIP interactions: 15 interactions with chain L Hydrophobic interactions: L:D.54, L:I.133, L:I.133, L:A.136, L:A.137, L:A.140, L:Q.148 Hydrogen bonds: L:D.54, L:S.147, L:S.147, L:S.147, L:Q.148, L:R.149 Water bridges: L:A.136 Salt bridges: L:R.129

Links

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Citation

Contreras-Martel, C. et al., Crystallization and 2.2 A resolution structure of R-phycoerythrin from Gracilaria chilensis: a case of perfect hemihedral twinning. Acta Crystallogr.,Sect.D (2001)

Release Date

2000-11-22

Peptides

R-PHYCOERYTHRIN: ACEGIK
R-PHYCOERYTHRIN: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
K

E
A

G
K

I
A

K
K

B
B

D
L

F
B

H
L

J
B

L
L

R-PHYCOERYTHRIN

R-PHYCOERYTHRIN

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