SMTL ID : 1qgw.1

CRYSTAL STRUCTURE OF PHYCOERYTHRIN 545 FROM THE MARINE CRYPTOPHYTE RHODOMONAS CS24

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

hetero-1-1-2-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 1 residues within 4Å: Chain A: N.76 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Chain D: D.107 No protein-ligand interaction detected (PLIP)

2 x DBV: 15,16-DIHYDROBILIVERDIN(Covalent)

DBV.2: 24 residues within 4Å: Chain A: F.14, C.19, S.20, R.21, P.23, K.24, E.25, S.26, D.36, E.37, M.38, M.39, K.41 Chain B: L.62, M.65, T.66, K.67 Chain C: Y.18, G.20 Chain D: P.64, S.65, I.67, S.68, P.69 21 PLIP interactions: 17 interactions with chain A, 2 interactions with chain D, 1 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: A:F.14, A:F.14, A:P.23, A:E.25, A:M.39, D:P.64, D:I.67, C:Y.18, B:L.62 Hydrogen bonds: A:R.21, A:K.24, A:E.25, A:E.25, A:E.25, A:S.26 Water bridges: A:H.16, A:R.21, A:K.24, A:K.41 Salt bridges: A:R.21, A:K.41 DBV.3: 21 residues within 4Å: Chain A: I.62, F.64, N.76 Chain B: F.14, H.16, C.19, S.20, R.21, P.23, K.24, E.25, Y.26, D.36, E.37, M.38, M.39, K.41 Chain C: S.65, I.67, S.68, P.69 23 PLIP interactions: 1 interactions with chain C, 20 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: C:I.67, B:F.14, B:F.14, B:F.14, B:R.21, B:P.23, B:E.25, B:Y.26, B:M.39, A:I.62, A:F.64 Hydrogen bonds: B:H.16, B:R.21, B:K.24, B:E.25, B:E.25, B:E.25, B:Y.26 Water bridges: B:K.41, B:K.41, B:K.41 Salt bridges: B:R.21, B:K.41

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 4 residues within 4Å: Chain A: I.68 Chain C: S.147, Q.148 Ligands: PEB.9 Ligand excluded by PLIP

6 x PEB: PHYCOERYTHROBILIN(Covalent)

PEB.5: 26 residues within 4Å: Chain A: F.64, E.65, K.66, D.69, G.70, P.71, F.72, T.73, S.74 Chain C: C.50, D.54, S.57, G.58, C.61, E.62, R.129, I.133, A.136, C.137, A.140, F.141, T.145, A.146, S.147, Q.148 Ligands: PEB.9 27 PLIP interactions: 18 interactions with chain C, 9 interactions with chain A Hydrophobic interactions: C:D.54, C:A.136, C:A.140, C:F.141, C:F.141, C:A.146, A:K.66, A:D.69, A:F.72, A:T.73 Hydrogen bonds: C:D.54, C:T.145, C:S.147, C:Q.148, A:D.69, A:P.71, A:T.73, A:S.74 Water bridges: C:R.129, C:R.129, C:R.129, C:A.136, C:A.136, C:S.147, C:S.147, A:D.69 Salt bridges: C:R.129 PEB.6: 27 residues within 4Å: Chain A: M.2, K.4, S.5, A.6, K.7 Chain C: M.59, L.66, N.72, C.73, R.77, R.78, A.81, C.82, R.84, D.85, I.88, Y.92, R.108, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, N.127, A.130 24 PLIP interactions: 23 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:R.78, C:A.81, C:I.88, C:I.88, C:Y.92, C:T.116, C:L.120, C:V.122, C:N.127, C:A.130 Hydrogen bonds: C:R.84, C:D.85, A:A.6 Water bridges: C:R.77, C:R.77, C:R.78, C:R.84, C:R.84, C:R.84, C:L.120 Salt bridges: C:R.77, C:R.78, C:R.84 pi-Cation interactions: C:R.84 PEB.7: 21 residues within 4Å: Chain A: I.13, D.15, R.17, Q.34, M.38, M.39 Chain C: L.24, K.28, N.35, K.36, L.38, D.39, S.40, V.142, N.143, N.144, T.153, P.154, Q.155, G.156, C.158 26 PLIP interactions: 18 interactions with chain C, 8 interactions with chain A Hydrophobic interactions: C:L.24, C:N.35, C:K.36, C:L.38, C:D.39, C:N.144, C:T.153, C:P.154, C:P.154, A:D.15, A:M.38 Hydrogen bonds: C:K.28, C:N.35, C:D.39, C:D.39, C:P.154, C:G.156, A:Q.34 Water bridges: C:N.35, C:N.35, C:K.36, A:R.17, A:R.17, A:R.17, A:R.17 Salt bridges: A:R.17 PEB.9: 20 residues within 4Å: Chain A: G.67, I.68 Chain B: K.64 Chain C: C.50, Q.148 Chain D: N.47, C.50, D.54, S.57, G.58, C.61, E.62, R.129, I.133, A.136, C.137, A.140, F.141 Ligands: CL.4, PEB.5 16 PLIP interactions: 2 interactions with chain B, 10 interactions with chain D, 2 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: B:K.64, B:K.64, D:I.133, D:A.136, D:A.140, D:F.141, D:F.141 Hydrogen bonds: D:D.54, D:D.54, A:I.68, C:Q.148 Water bridges: D:R.129, D:R.129, A:D.69, C:S.147 Salt bridges: D:R.129 PEB.10: 26 residues within 4Å: Chain B: M.2, K.4, S.5, A.6, K.7 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, T.116, Y.117, L.120, V.122, P.123, S.126, N.127, A.130 14 PLIP interactions: 1 interactions with chain B, 13 interactions with chain D Hydrogen bonds: B:A.6, D:R.84, D:D.85 Hydrophobic interactions: D:I.88, D:I.88, D:T.116, D:L.120, D:V.122, D:N.127, D:A.130 Water bridges: D:R.84 Salt bridges: D:R.77, D:R.84 pi-Cation interactions: D:R.84 PEB.11: 20 residues within 4Å: Chain B: I.13, D.15, R.17, M.38, M.39 Chain D: L.24, K.28, N.35, K.36, L.38, D.39, S.40, V.142, N.144, L.151, T.153, P.154, Q.155, G.156, C.158 22 PLIP interactions: 15 interactions with chain D, 7 interactions with chain B Hydrophobic interactions: D:L.24, D:N.35, D:L.38, D:L.38, D:D.39, D:P.154, B:D.15 Hydrogen bonds: D:K.28, D:N.35, D:D.39, D:D.39, D:T.153, D:P.154, D:G.156 Water bridges: D:K.36, B:R.17, B:R.17, B:R.17, B:R.17, B:R.17 Salt bridges: D:K.36, B:R.17

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wilk, K.E. et al., Evolution of a light-harvesting protein by addition of new subunits and rearrangement of conserved elements: crystal structure of a cryptophyte phycoerythrin at 1.63-A resolution. Proc.Natl.Acad.Sci.USA (1999)

Release Date

1999-05-19

Peptides

PROTEIN (CRYPTOPHYTAN PHYCOERYTHRIN (ALPHA-1 CHAIN)): A
PROTEIN (CRYPTOPHYTAN PHYCOERYTHRIN (ALPHA-2 CHAIN)): B
PROTEIN (CRYPTOPHYTAN PHYCOERYTHRIN (BETA CHAIN)): CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

PROTEIN (CRYPTOPHYTAN PHYCOERYTHRIN (ALPHA-1 CHAIN))

PROTEIN (CRYPTOPHYTAN PHYCOERYTHRIN (ALPHA-2 CHAIN))

PROTEIN (CRYPTOPHYTAN PHYCOERYTHRIN (BETA CHAIN))

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