SMTL ID : 4z8k.1

Phycocyanin structure from T. elongatus at 2.5-A from XFEL using a viscous delivery medium for serial femtosecond crystallography

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

hetero-3-3-mer

Ligands

9 x CYC: PHYCOCYANOBILIN(Covalent)

CYC.1: 31 residues within 4Å: Chain A: V.59, Y.60, T.66, S.72, Q.73, Y.74, A.75, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, M.94, Y.110, L.111, L.115, I.118, F.122, L.124, W.128, Y.129 Chain F: R.57, F.60, I.67, Y.74, T.75, N.76, M.79 26 PLIP interactions: 23 interactions with chain A, 3 interactions with chain F Hydrophobic interactions: A:V.59, A:T.66, A:K.83, A:K.83, A:I.88, A:Y.90, A:L.111, A:I.118, A:F.122, A:W.128, A:W.128, A:Y.129, F:Y.74 Hydrogen bonds: A:S.72, A:Q.73, A:A.75, A:R.86, A:D.87, A:Y.129, F:T.75 Water bridges: A:S.72 Salt bridges: A:K.83, A:R.86, F:R.57 pi-Stacking: A:Y.90 pi-Cation interactions: A:R.86 CYC.2: 27 residues within 4Å: Chain B: L.59, F.60, L.66, N.72, A.73, R.77, R.78, M.79, A.81, C.82, R.84, D.85, M.86, I.88, I.89, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, T.122, P.123, S.126, V.127, A.130 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:L.59, B:L.66, B:R.78, B:R.78, B:A.81, B:I.88, B:I.88, B:L.113, B:L.120, B:T.122, B:V.127, B:A.130 Hydrogen bonds: B:R.84, B:D.85, B:T.122, B:T.122 Salt bridges: B:R.77, B:R.84 pi-Cation interactions: B:R.84 CYC.3: 24 residues within 4Å: Chain A: N.21, L.24, Q.25, D.28 Chain B: K.32, E.33, N.35, K.36, L.38, D.39, A.40, N.42, R.43, A.142, N.143, D.144, P.145, I.148, T.149, P.150, G.151, C.153, L.156, M.157 12 PLIP interactions: 11 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:N.35, B:L.38, B:I.148, A:L.24 Hydrogen bonds: B:N.35, B:D.39, B:T.149, B:T.149, B:G.151 Water bridges: B:N.35, B:N.35, B:T.149 CYC.4: 31 residues within 4Å: Chain B: R.57, F.60, I.67, Y.74, T.75, N.76, M.79 Chain C: V.59, Y.60, T.66, S.72, Q.73, Y.74, A.75, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, M.94, Y.110, L.111, L.115, I.118, F.122, L.124, W.128, Y.129 26 PLIP interactions: 23 interactions with chain C, 3 interactions with chain B Hydrophobic interactions: C:V.59, C:T.66, C:K.83, C:K.83, C:I.88, C:Y.90, C:L.111, C:I.118, C:F.122, C:W.128, C:W.128, C:Y.129, B:Y.74 Hydrogen bonds: C:S.72, C:Q.73, C:A.75, C:R.86, C:D.87, C:Y.129, B:T.75 Water bridges: C:S.72 Salt bridges: C:K.83, C:R.86, B:R.57 pi-Stacking: C:Y.90 pi-Cation interactions: C:R.86 CYC.5: 27 residues within 4Å: Chain D: L.59, F.60, L.66, N.72, A.73, R.77, R.78, M.79, A.81, C.82, R.84, D.85, M.86, I.88, I.89, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, T.122, P.123, S.126, V.127, A.130 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:L.59, D:L.66, D:R.78, D:R.78, D:A.81, D:I.88, D:I.88, D:L.113, D:L.120, D:T.122, D:V.127, D:A.130 Hydrogen bonds: D:R.84, D:D.85, D:T.122, D:T.122 Salt bridges: D:R.77, D:R.84 pi-Cation interactions: D:R.84 CYC.6: 24 residues within 4Å: Chain C: N.21, L.24, Q.25, D.28 Chain D: K.32, E.33, N.35, K.36, L.38, D.39, A.40, N.42, R.43, A.142, N.143, D.144, P.145, I.148, T.149, P.150, G.151, C.153, L.156, M.157 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:N.35, D:L.38, D:I.148, C:L.24 Hydrogen bonds: D:N.35, D:D.39, D:T.149, D:T.149, D:G.151 Water bridges: D:N.35, D:N.35, D:T.149 CYC.7: 31 residues within 4Å: Chain D: R.57, F.60, I.67, Y.74, T.75, N.76, M.79 Chain E: V.59, Y.60, T.66, S.72, Q.73, Y.74, A.75, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, M.94, Y.110, L.111, L.115, I.118, F.122, L.124, W.128, Y.129 26 PLIP interactions: 23 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:V.59, E:T.66, E:K.83, E:K.83, E:I.88, E:Y.90, E:L.111, E:I.118, E:F.122, E:W.128, E:W.128, E:Y.129, D:Y.74 Hydrogen bonds: E:S.72, E:Q.73, E:A.75, E:R.86, E:D.87, E:Y.129, D:T.75 Water bridges: E:S.72 Salt bridges: E:K.83, E:R.86, D:R.57 pi-Stacking: E:Y.90 pi-Cation interactions: E:R.86 CYC.8: 27 residues within 4Å: Chain F: L.59, F.60, L.66, N.72, A.73, R.77, R.78, M.79, A.81, C.82, R.84, D.85, M.86, I.88, I.89, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, T.122, P.123, S.126, V.127, A.130 19 PLIP interactions: 19 interactions with chain F Hydrophobic interactions: F:L.59, F:L.66, F:R.78, F:R.78, F:A.81, F:I.88, F:I.88, F:L.113, F:L.120, F:T.122, F:V.127, F:A.130 Hydrogen bonds: F:R.84, F:D.85, F:T.122, F:T.122 Salt bridges: F:R.77, F:R.84 pi-Cation interactions: F:R.84 CYC.9: 24 residues within 4Å: Chain E: N.21, L.24, Q.25, D.28 Chain F: K.32, E.33, N.35, K.36, L.38, D.39, A.40, N.42, R.43, A.142, N.143, D.144, P.145, I.148, T.149, P.150, G.151, C.153, L.156, M.157 12 PLIP interactions: 1 interactions with chain E, 11 interactions with chain F Hydrophobic interactions: E:L.24, F:N.35, F:L.38, F:I.148 Hydrogen bonds: F:N.35, F:D.39, F:T.149, F:T.149, F:G.151 Water bridges: F:N.35, F:N.35, F:T.149

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Conrad, C.E. et al., A novel inert crystal delivery medium for serial femtosecond crystallography. Iucrj (2015)

Release Date

2015-08-12

Peptides

C-phycocyanin alpha chain: ACE
C-phycocyanin beta chain: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

E
A

B
B

D
B

F
B

C-phycocyanin alpha chain

C-phycocyanin beta chain

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