SMTL ID : 1lia.5 (5 other biounits)

CRYSTAL STRUCTURE OF R-PHYCOERYTHRIN FROM POLYSIPHONIA AT 2.8 A RESOLUTION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

hetero-oligomer

Ligands

12 x CYC: PHYCOCYANOBILIN(Covalent)

CYC.1: 24 residues within 4Å: Chain A: F.60, N.66, A.72, G.73, K.78, K.81, C.82, R.84, D.85, H.88, Y.89, L.92, W.108, Y.117, L.120, L.122, P.123, A.126, Y.127 Chain F: I.67, Y.74, T.75, N.76, M.79 24 PLIP interactions: 21 interactions with chain A, 3 interactions with chain F Hydrophobic interactions: A:A.72, A:K.78, A:K.81, A:K.81, A:H.88, A:Y.89, A:L.92, A:L.120, A:L.122, A:A.126, A:Y.127, A:Y.127, F:Y.74, F:M.79 Hydrogen bonds: A:K.78, A:R.84, A:D.85, A:D.85, A:Y.127, F:T.75 Salt bridges: A:K.78, A:K.81, A:K.81, A:R.84 CYC.2: 13 residues within 4Å: Chain A: K.43, L.44, N.47, A.50, V.51, E.54, T.134, R.137, L.138, C.139, R.142, D.143, M.144 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:K.43, A:A.50, A:V.51 Hydrogen bonds: A:N.47, A:D.143, A:D.143 Salt bridges: A:R.137, A:R.142 CYC.4: 16 residues within 4Å: Chain A: L.24, Q.25, Q.28 Chain B: N.32, N.35, K.36, L.38, D.39, I.142, S.143, N.144, V.153, I.154, E.155, G.156, C.158 16 PLIP interactions: 13 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:K.36, B:L.38, B:L.38, B:N.144, B:V.153, B:V.153, B:I.154, A:L.24, A:Q.25 Hydrogen bonds: B:N.35, B:N.35, B:K.36, B:D.39, B:I.154, B:G.156, A:Q.28 CYC.5: 19 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 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:R.78, B:A.81, B:I.88, B:I.88, B:L.113, B:L.120, B:V.122, B:V.122 Hydrogen bonds: B:N.72, B:N.72, B:R.84, B:D.85 Salt bridges: B:R.77, B:R.84 CYC.6: 24 residues within 4Å: Chain B: I.67, Y.74, T.75, N.76, M.79 Chain C: F.60, N.66, A.72, G.73, K.78, K.81, C.82, R.84, D.85, H.88, Y.89, L.92, W.108, Y.117, L.120, L.122, P.123, A.126, Y.127 24 PLIP interactions: 21 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:A.72, C:K.78, C:K.81, C:K.81, C:H.88, C:Y.89, C:L.92, C:L.120, C:L.122, C:A.126, C:Y.127, C:Y.127, B:Y.74, B:M.79 Hydrogen bonds: C:K.78, C:R.84, C:D.85, C:D.85, C:Y.127, B:T.75 Salt bridges: C:K.78, C:K.81, C:K.81, C:R.84 CYC.7: 13 residues within 4Å: Chain C: K.43, L.44, N.47, A.50, V.51, E.54, T.134, R.137, L.138, C.139, R.142, D.143, M.144 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:K.43, C:A.50, C:V.51 Hydrogen bonds: C:N.47, C:D.143, C:D.143 Salt bridges: C:R.137, C:R.142 CYC.9: 16 residues within 4Å: Chain C: L.24, Q.25, Q.28 Chain D: N.32, N.35, K.36, L.38, D.39, I.142, S.143, N.144, V.153, I.154, E.155, G.156, C.158 16 PLIP interactions: 13 interactions with chain D, 3 interactions with chain C Hydrophobic interactions: D:K.36, D:L.38, D:L.38, D:N.144, D:V.153, D:V.153, D:I.154, C:L.24, C:Q.25 Hydrogen bonds: D:N.35, D:N.35, D:K.36, D:D.39, D:I.154, D:G.156, C:Q.28 CYC.10: 19 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, L.113, Y.117, L.120, V.122, P.123, S.126, T.127 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:R.78, D:A.81, D:I.88, D:I.88, D:L.113, D:L.120, D:V.122, D:V.122 Hydrogen bonds: D:N.72, D:N.72, D:R.84, D:D.85 Salt bridges: D:R.77, D:R.84 CYC.11: 24 residues within 4Å: Chain D: I.67, Y.74, T.75, N.76, M.79 Chain E: F.60, N.66, A.72, G.73, K.78, K.81, C.82, R.84, D.85, H.88, Y.89, L.92, W.108, Y.117, L.120, L.122, P.123, A.126, Y.127 24 PLIP interactions: 21 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:A.72, E:K.78, E:K.81, E:K.81, E:H.88, E:Y.89, E:L.92, E:L.120, E:L.122, E:A.126, E:Y.127, E:Y.127, D:Y.74, D:M.79 Hydrogen bonds: E:K.78, E:R.84, E:D.85, E:D.85, E:Y.127, D:T.75 Salt bridges: E:K.78, E:K.81, E:K.81, E:R.84 CYC.12: 13 residues within 4Å: Chain E: K.43, L.44, N.47, A.50, V.51, E.54, T.134, R.137, L.138, C.139, R.142, D.143, M.144 8 PLIP interactions: 8 interactions with chain E Hydrophobic interactions: E:K.43, E:A.50, E:V.51 Hydrogen bonds: E:N.47, E:D.143, E:D.143 Salt bridges: E:R.137, E:R.142 CYC.14: 16 residues within 4Å: Chain E: L.24, Q.25, Q.28 Chain F: N.32, N.35, K.36, L.38, D.39, I.142, S.143, N.144, V.153, I.154, E.155, G.156, C.158 16 PLIP interactions: 3 interactions with chain E, 13 interactions with chain F Hydrophobic interactions: E:L.24, E:Q.25, F:K.36, F:L.38, F:L.38, F:N.144, F:V.153, F:V.153, F:I.154 Hydrogen bonds: E:Q.28, F:N.35, F:N.35, F:K.36, F:D.39, F:I.154, F:G.156 CYC.15: 19 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 14 PLIP interactions: 14 interactions with chain F Hydrophobic interactions: F:R.78, F:A.81, F:I.88, F:I.88, F:L.113, F:L.120, F:V.122, F:V.122 Hydrogen bonds: F:N.72, F:N.72, F:R.84, F:D.85 Salt bridges: F:R.77, F:R.84

3 x PUB: PHYCOUROBILIN(Covalent)

PUB.3: 17 residues within 4Å: Chain B: C.50, D.54, S.57, G.58, C.61, E.62, R.129, I.133, A.136, A.137, C.140, F.141, T.145, A.146, S.147, Q.148, R.149 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:I.133, B:A.136, B:A.137, B:F.141, B:F.141, B:A.146, B:Q.148 Hydrogen bonds: B:D.54, B:E.62, B:T.145, B:S.147, B:S.147, B:Q.148, B:Q.148, B:R.149 Salt bridges: B:R.129 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, A.137, C.140, F.141, T.145, A.146, S.147, Q.148, R.149 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:I.133, D:A.136, D:A.137, D:F.141, D:F.141, D:A.146, D:Q.148 Hydrogen bonds: D:D.54, D:E.62, D:T.145, D:S.147, D:S.147, D:Q.148, D:Q.148, D:R.149 Salt bridges: D:R.129 PUB.13: 17 residues within 4Å: Chain F: C.50, D.54, S.57, G.58, C.61, E.62, R.129, I.133, A.136, A.137, C.140, F.141, T.145, A.146, S.147, Q.148, R.149 16 PLIP interactions: 16 interactions with chain F Hydrophobic interactions: F:I.133, F:A.136, F:A.137, F:F.141, F:F.141, F:A.146, F:Q.148 Hydrogen bonds: F:D.54, F:E.62, F:T.145, F:S.147, F:S.147, F:Q.148, F:Q.148, F:R.149 Salt bridges: F:R.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chang, W.R. et al., Crystal structure of R-phycoerythrin from Polysiphonia urceolata at 2.8 A resolution. J.Mol.Biol. (1996)

Release Date

1997-07-29

Peptides

R-PHYCOERYTHRIN: ACE
R-PHYCOERYTHRIN: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
K

C
K

E
K

B
L

D
L

F
L

R-PHYCOERYTHRIN

R-PHYCOERYTHRIN

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