SMTL ID : 2vjh.1

The structure of Phycoerythrin from Gloeobacter violaceus

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

hetero-6-6-mer

Ligands

24 x PEB: PHYCOERYTHROBILIN(Covalent)

PEB.1: 25 residues within 4Å: Chain A: F.60, L.66, A.72, G.73, K.78, K.81, C.82, R.84, D.85, H.88, Y.89, W.108, V.116, Y.117, L.120, L.122, P.123, A.126, Y.127 Chain F: I.60, I.67, Y.74, T.75, N.76, M.79 29 PLIP interactions: 6 interactions with chain F, 23 interactions with chain A Hydrophobic interactions: F:I.60, F:Y.74, F:M.79, A:A.72, A:K.78, A:K.81, A:K.81, A:H.88, A:Y.89, A:V.116, A:L.120, A:L.122, A:A.126, A:Y.127 Hydrogen bonds: F:T.75, A:A.72, A:R.84, A:D.85, A:Y.127 Water bridges: F:S.57, F:S.57, A:K.78, A:K.81, A:K.81, A:L.120 Salt bridges: A:K.78, A:K.81, A:R.84 pi-Cation interactions: A:H.88 PEB.2: 13 residues within 4Å: Chain A: K.43, L.44, G.47, A.50, V.51, E.54, R.137, A.138, C.139, R.142, D.143, M.144, F.152 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.50, A:V.51, A:A.138, A:D.143, A:F.152 Hydrogen bonds: A:R.142 Water bridges: A:R.137, A:R.137, A:D.143, A:D.143 Salt bridges: A:R.137, A:R.142 pi-Cation interactions: A:R.142 PEB.4: 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, T.116, Y.117, L.120, V.122, P.123, S.126, A.127 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:R.78, B:A.81, B:I.88, B:T.116, B:L.120, B:V.122, B:V.122, B:A.127 Hydrogen bonds: B:R.84, B:D.85 Water bridges: B:R.77, B:R.77, B:R.77 Salt bridges: B:R.77, B:R.78, B:R.84 pi-Cation interactions: B:R.84 PEB.5: 19 residues within 4Å: Chain A: L.24, E.25, Q.28 Chain B: N.35, K.36, L.38, D.39, A.40, I.142, N.143, N.144, T.153, P.154, Q.155, G.156, D.157, C.158 Chain C: R.33, Q.147 21 PLIP interactions: 15 interactions with chain B, 2 interactions with chain A, 4 interactions with chain C Hydrophobic interactions: B:N.35, B:K.36, B:K.36, B:L.38, B:L.38, B:D.39, B:N.144, B:P.154, B:P.154, A:L.24, C:R.33 Hydrogen bonds: B:N.35, B:D.39, B:T.153, B:P.154, B:G.156, A:Q.28, C:Q.147 Water bridges: B:K.36, C:R.33 pi-Cation interactions: C:R.33 PEB.6: 25 residues within 4Å: Chain C: F.60, L.66, A.72, G.73, K.78, K.81, C.82, R.84, D.85, H.88, Y.89, W.108, V.116, Y.117, L.120, L.122, P.123, A.126, Y.127 Chain L: I.60, I.67, Y.74, T.75, N.76, M.79 28 PLIP interactions: 22 interactions with chain C, 6 interactions with chain L Hydrophobic interactions: C:A.72, C:K.78, C:K.81, C:K.81, C:Y.89, C:V.116, C:L.120, C:L.122, C:A.126, C:Y.127, L:I.60, L:I.67, L:Y.74, L:M.79 Hydrogen bonds: C:A.72, C:R.84, C:D.85, C:Y.127, L:T.75 Water bridges: C:K.78, C:R.84, C:H.88, C:L.120, L:S.57 Salt bridges: C:K.78, C:K.81, C:R.84 pi-Cation interactions: C:H.88 PEB.7: 12 residues within 4Å: Chain C: K.43, L.44, G.47, A.50, V.51, E.54, R.137, A.138, C.139, R.142, D.143, M.144 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:A.50, C:V.51, C:A.138, C:D.143 Hydrogen bonds: C:R.142 Water bridges: C:D.143, C:D.143 Salt bridges: C:R.137, C:R.142 pi-Cation interactions: C:R.142 PEB.9: 19 residues within 4Å: Chain D: M.59, N.72, C.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, R.108, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, A.127 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:R.78, D:A.81, D:I.88, D:I.88, D:T.116, D:L.120, D:A.127 Hydrogen bonds: D:R.84, D:R.84, D:D.85 Water bridges: D:R.77, D:R.78 Salt bridges: D:R.77, D:R.78, D:R.84 pi-Cation interactions: D:R.84 PEB.10: 19 residues within 4Å: Chain A: R.33, Q.147 Chain C: L.24, E.25, Q.28 Chain D: N.35, K.36, L.38, D.39, A.40, I.142, N.143, N.144, T.153, P.154, Q.155, G.156, D.157, C.158 27 PLIP interactions: 20 interactions with chain D, 4 interactions with chain A, 3 interactions with chain C Hydrophobic interactions: D:N.35, D:K.36, D:K.36, D:L.38, D:L.38, D:D.39, D:N.144, D:P.154, D:P.154, A:R.33, C:L.24, C:E.25 Hydrogen bonds: D:N.35, D:D.39, D:D.39, D:T.153, D:P.154, D:Q.155, D:G.156, A:Q.147, C:Q.28 Water bridges: D:N.35, D:K.36, D:K.36, D:K.36, A:R.33 pi-Cation interactions: A:R.33 PEB.11: 25 residues within 4Å: Chain E: F.60, L.66, A.72, G.73, K.78, K.81, C.82, R.84, D.85, H.88, Y.89, W.108, V.116, Y.117, L.120, L.122, P.123, A.126, Y.127 Chain J: I.60, I.67, Y.74, T.75, N.76, M.79 29 PLIP interactions: 23 interactions with chain E, 6 interactions with chain J Hydrophobic interactions: E:A.72, E:K.78, E:K.81, E:K.81, E:H.88, E:Y.89, E:V.116, E:L.120, E:L.122, E:A.126, E:Y.127, J:I.60, J:Y.74, J:M.79 Hydrogen bonds: E:A.72, E:R.84, E:D.85, E:Y.127, J:T.75 Water bridges: E:K.78, E:K.81, E:K.81, E:L.120, J:S.57, J:S.57 Salt bridges: E:K.78, E:K.81, E:R.84 pi-Cation interactions: E:H.88 PEB.12: 13 residues within 4Å: Chain E: K.43, L.44, G.47, A.50, V.51, E.54, R.137, A.138, C.139, R.142, D.143, M.144, F.152 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:A.50, E:V.51, E:A.138, E:D.143, E:F.152 Hydrogen bonds: E:R.142 Water bridges: E:R.137, E:R.137, E:D.143, E:D.143 Salt bridges: E:R.137, E:R.142 pi-Cation interactions: E:R.142 PEB.14: 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, T.116, Y.117, L.120, V.122, P.123, S.126, A.127 17 PLIP interactions: 17 interactions with chain F Hydrophobic interactions: F:R.78, F:A.81, F:I.88, F:T.116, F:L.120, F:V.122, F:V.122, F:A.127 Hydrogen bonds: F:R.84, F:D.85 Water bridges: F:R.77, F:R.77, F:R.77 Salt bridges: F:R.77, F:R.78, F:R.84 pi-Cation interactions: F:R.84 PEB.15: 19 residues within 4Å: Chain E: L.24, E.25, Q.28 Chain F: N.35, K.36, L.38, D.39, A.40, I.142, N.143, N.144, T.153, P.154, Q.155, G.156, D.157, C.158 Chain G: R.33, Q.147 21 PLIP interactions: 15 interactions with chain F, 2 interactions with chain E, 4 interactions with chain G Hydrophobic interactions: F:N.35, F:K.36, F:K.36, F:L.38, F:L.38, F:D.39, F:N.144, F:P.154, F:P.154, E:L.24, G:R.33 Hydrogen bonds: F:N.35, F:D.39, F:T.153, F:P.154, F:G.156, E:Q.28, G:Q.147 Water bridges: F:K.36, G:R.33 pi-Cation interactions: G:R.33 PEB.16: 25 residues within 4Å: Chain D: I.60, I.67, Y.74, T.75, N.76, M.79 Chain G: F.60, L.66, A.72, G.73, K.78, K.81, C.82, R.84, D.85, H.88, Y.89, W.108, V.116, Y.117, L.120, L.122, P.123, A.126, Y.127 28 PLIP interactions: 6 interactions with chain D, 22 interactions with chain G Hydrophobic interactions: D:I.60, D:I.67, D:Y.74, D:M.79, G:A.72, G:K.78, G:K.81, G:K.81, G:Y.89, G:V.116, G:L.120, G:L.122, G:A.126, G:Y.127 Hydrogen bonds: D:T.75, G:A.72, G:R.84, G:D.85, G:Y.127 Water bridges: D:S.57, G:K.78, G:R.84, G:H.88, G:L.120 Salt bridges: G:K.78, G:K.81, G:R.84 pi-Cation interactions: G:H.88 PEB.17: 12 residues within 4Å: Chain G: K.43, L.44, G.47, A.50, V.51, E.54, R.137, A.138, C.139, R.142, D.143, M.144 9 PLIP interactions: 9 interactions with chain G Hydrophobic interactions: G:A.50, G:V.51, G:A.138, G:D.143 Hydrogen bonds: G:R.142 Water bridges: G:D.143 Salt bridges: G:R.137, G:R.142 pi-Cation interactions: G:R.142 PEB.19: 19 residues within 4Å: Chain H: M.59, N.72, C.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, R.108, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, A.127 16 PLIP interactions: 16 interactions with chain H Hydrophobic interactions: H:R.78, H:A.81, H:I.88, H:I.88, H:T.116, H:L.120, H:A.127 Hydrogen bonds: H:R.84, H:R.84, H:D.85 Water bridges: H:R.77, H:R.78 Salt bridges: H:R.77, H:R.78, H:R.84 pi-Cation interactions: H:R.84 PEB.20: 19 residues within 4Å: Chain E: R.33, Q.147 Chain G: L.24, E.25, Q.28 Chain H: N.35, K.36, L.38, D.39, A.40, I.142, N.143, N.144, T.153, P.154, Q.155, G.156, D.157, C.158 26 PLIP interactions: 19 interactions with chain H, 4 interactions with chain E, 3 interactions with chain G Hydrophobic interactions: H:N.35, H:K.36, H:K.36, H:L.38, H:L.38, H:D.39, H:N.144, H:P.154, H:P.154, E:R.33, G:L.24, G:E.25 Hydrogen bonds: H:N.35, H:D.39, H:T.153, H:P.154, H:Q.155, H:G.156, E:Q.147, G:Q.28 Water bridges: H:N.35, H:K.36, H:K.36, H:K.36, E:R.33 pi-Cation interactions: E:R.33 PEB.21: 25 residues within 4Å: Chain B: I.60, I.67, Y.74, T.75, N.76, M.79 Chain I: F.60, L.66, A.72, G.73, K.78, K.81, C.82, R.84, D.85, H.88, Y.89, W.108, V.116, Y.117, L.120, L.122, P.123, A.126, Y.127 29 PLIP interactions: 23 interactions with chain I, 6 interactions with chain B Hydrophobic interactions: I:A.72, I:K.78, I:K.81, I:K.81, I:H.88, I:Y.89, I:V.116, I:L.120, I:L.122, I:A.126, I:Y.127, B:I.60, B:Y.74, B:M.79 Hydrogen bonds: I:A.72, I:R.84, I:D.85, I:Y.127, B:T.75 Water bridges: I:K.78, I:K.81, I:K.81, I:L.120, B:S.57, B:S.57 Salt bridges: I:K.78, I:K.81, I:R.84 pi-Cation interactions: I:H.88 PEB.22: 13 residues within 4Å: Chain I: K.43, L.44, G.47, A.50, V.51, E.54, R.137, A.138, C.139, R.142, D.143, M.144, F.152 13 PLIP interactions: 13 interactions with chain I Hydrophobic interactions: I:A.50, I:V.51, I:A.138, I:D.143, I:F.152 Hydrogen bonds: I:R.142 Water bridges: I:R.137, I:R.137, I:D.143, I:D.143 Salt bridges: I:R.137, I:R.142 pi-Cation interactions: I:R.142 PEB.24: 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, T.116, Y.117, L.120, V.122, P.123, S.126, A.127 17 PLIP interactions: 17 interactions with chain J Hydrophobic interactions: J:R.78, J:A.81, J:I.88, J:T.116, J:L.120, J:V.122, J:V.122, J:A.127 Hydrogen bonds: J:R.84, J:D.85 Water bridges: J:R.77, J:R.77, J:R.77 Salt bridges: J:R.77, J:R.78, J:R.84 pi-Cation interactions: J:R.84 PEB.25: 19 residues within 4Å: Chain I: L.24, E.25, Q.28 Chain J: N.35, K.36, L.38, D.39, A.40, I.142, N.143, N.144, T.153, P.154, Q.155, G.156, D.157, C.158 Chain K: R.33, Q.147 22 PLIP interactions: 2 interactions with chain I, 16 interactions with chain J, 4 interactions with chain K Hydrophobic interactions: I:L.24, J:N.35, J:K.36, J:K.36, J:L.38, J:L.38, J:D.39, J:N.144, J:P.154, J:P.154, K:R.33 Hydrogen bonds: I:Q.28, J:N.35, J:D.39, J:D.39, J:T.153, J:P.154, J:G.156, K:Q.147 Water bridges: J:K.36, K:R.33 pi-Cation interactions: K:R.33 PEB.26: 25 residues within 4Å: Chain H: I.60, I.67, Y.74, T.75, N.76, M.79 Chain K: F.60, L.66, A.72, G.73, K.78, K.81, C.82, R.84, D.85, H.88, Y.89, W.108, V.116, Y.117, L.120, L.122, P.123, A.126, Y.127 28 PLIP interactions: 22 interactions with chain K, 6 interactions with chain H Hydrophobic interactions: K:A.72, K:K.78, K:K.81, K:K.81, K:Y.89, K:V.116, K:L.120, K:L.122, K:A.126, K:Y.127, H:I.60, H:I.67, H:Y.74, H:M.79 Hydrogen bonds: K:A.72, K:R.84, K:D.85, K:Y.127, H:T.75 Water bridges: K:K.78, K:R.84, K:H.88, K:L.120, H:S.57 Salt bridges: K:K.78, K:K.81, K:R.84 pi-Cation interactions: K:H.88 PEB.27: 12 residues within 4Å: Chain K: K.43, L.44, G.47, A.50, V.51, E.54, R.137, A.138, C.139, R.142, D.143, M.144 10 PLIP interactions: 10 interactions with chain K Hydrophobic interactions: K:A.50, K:V.51, K:A.138, K:D.143 Hydrogen bonds: K:R.142 Water bridges: K:D.143, K:D.143 Salt bridges: K:R.137, K:R.142 pi-Cation interactions: K:R.142 PEB.29: 19 residues within 4Å: Chain L: M.59, N.72, C.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, R.108, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, A.127 16 PLIP interactions: 16 interactions with chain L Hydrophobic interactions: L:R.78, L:A.81, L:I.88, L:I.88, L:T.116, L:L.120, L:A.127 Hydrogen bonds: L:R.84, L:R.84, L:D.85 Water bridges: L:R.77, L:R.78 Salt bridges: L:R.77, L:R.78, L:R.84 pi-Cation interactions: L:R.84 PEB.30: 19 residues within 4Å: Chain I: R.33, Q.147 Chain K: L.24, E.25, Q.28 Chain L: N.35, K.36, L.38, D.39, A.40, I.142, N.143, N.144, T.153, P.154, Q.155, G.156, D.157, C.158 27 PLIP interactions: 20 interactions with chain L, 3 interactions with chain K, 4 interactions with chain I Hydrophobic interactions: L:N.35, L:K.36, L:K.36, L:L.38, L:L.38, L:D.39, L:N.144, L:P.154, L:P.154, K:L.24, K:E.25, I:R.33 Hydrogen bonds: L:N.35, L:D.39, L:D.39, L:T.153, L:P.154, L:Q.155, L:G.156, K:Q.28, I:Q.147 Water bridges: L:N.35, L:K.36, L:K.36, L:K.36, I:R.33 pi-Cation interactions: I:R.33

6 x PUB: PHYCOUROBILIN(Covalent)

PUB.3: 16 residues within 4Å: Chain B: C.50, D.54, S.57, G.58, C.61, E.62, R.129, I.133, A.136, S.137, F.141, T.145, A.146, S.147, K.148, R.149 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:I.133, B:A.136, B:F.141, B:A.146, B:R.149 Hydrogen bonds: B:D.54, B:S.147, B:K.148, B:R.149 Water bridges: B:R.129, B:A.136, B:S.137 Salt bridges: B:R.129 pi-Stacking: B:F.141 pi-Cation interactions: B:K.148 PUB.8: 17 residues within 4Å: Chain D: C.50, D.54, S.57, G.58, C.61, E.62, R.129, I.133, A.136, S.137, A.140, F.141, T.145, A.146, S.147, K.148, R.149 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:I.133, D:A.136, D:F.141, D:A.146, D:R.149 Hydrogen bonds: D:D.54, D:S.147, D:K.148, D:R.149 Water bridges: D:D.54, D:R.129, D:R.129, D:A.136 Salt bridges: D:R.129 pi-Stacking: D:F.141 pi-Cation interactions: D:K.148 PUB.13: 16 residues within 4Å: Chain F: C.50, D.54, S.57, G.58, C.61, E.62, R.129, I.133, A.136, S.137, F.141, T.145, A.146, S.147, K.148, R.149 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:I.133, F:A.136, F:F.141, F:A.146, F:R.149 Hydrogen bonds: F:D.54, F:S.147, F:K.148, F:R.149 Water bridges: F:R.129, F:A.136, F:S.137 Salt bridges: F:R.129 pi-Stacking: F:F.141 pi-Cation interactions: F:K.148 PUB.18: 17 residues within 4Å: Chain H: C.50, D.54, S.57, G.58, C.61, E.62, R.129, I.133, A.136, S.137, A.140, F.141, T.145, A.146, S.147, K.148, R.149 16 PLIP interactions: 16 interactions with chain H Hydrophobic interactions: H:I.133, H:A.136, H:F.141, H:A.146, H:R.149 Hydrogen bonds: H:D.54, H:S.147, H:K.148, H:R.149 Water bridges: H:R.129, H:R.129, H:A.136, H:S.137 Salt bridges: H:R.129 pi-Stacking: H:F.141 pi-Cation interactions: H:K.148 PUB.23: 16 residues within 4Å: Chain J: C.50, D.54, S.57, G.58, C.61, E.62, R.129, I.133, A.136, S.137, F.141, T.145, A.146, S.147, K.148, R.149 15 PLIP interactions: 15 interactions with chain J Hydrophobic interactions: J:I.133, J:A.136, J:F.141, J:A.146, J:R.149 Hydrogen bonds: J:D.54, J:S.147, J:K.148, J:R.149 Water bridges: J:D.54, J:R.129, J:A.136 Salt bridges: J:R.129 pi-Stacking: J:F.141 pi-Cation interactions: J:K.148 PUB.28: 17 residues within 4Å: Chain L: C.50, D.54, S.57, G.58, C.61, E.62, R.129, I.133, A.136, S.137, A.140, F.141, T.145, A.146, S.147, K.148, R.149 17 PLIP interactions: 17 interactions with chain L Hydrophobic interactions: L:I.133, L:A.136, L:F.141, L:A.146, L:R.149 Hydrogen bonds: L:D.54, L:S.147, L:K.148, L:R.149 Water bridges: L:E.62, L:R.129, L:R.129, L:A.136, L:S.137 Salt bridges: L:R.129 pi-Stacking: L:F.141 pi-Cation interactions: L:K.148

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Murray, J.W. et al., The Structures of the Phycobiliproteins of Gloeobacter Violaceus. To be Published

Release Date

2008-03-25

Peptides

PHYCOERYTHRIN ALPHA CHAIN: ACEGIK
PHYCOERYTHRIN BETA SUBUNIT: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
A

G
C

I
A

K
C

B
B

D
D

F
B

H
D

J
B

L
D

PHYCOERYTHRIN ALPHA CHAIN

PHYCOERYTHRIN BETA SUBUNIT