SMTL ID : 8b4n.1

X-ray structure of phycoerythrin from Porphyridium cruentum

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

hetero-6-6-mer

Ligands

30 x PEB: PHYCOERYTHROBILIN(Non-covalent)

PEB.1: 23 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 J: I.67, T.75, N.76, M.79 30 PLIP interactions: 26 interactions with chain A, 4 interactions with chain J Hydrophobic interactions: A:L.66, A:A.72, A:K.78, A:K.81, A:K.81, A:D.85, A:H.88, A:Y.89, A:V.116, A:L.120, A:A.126, A:Y.127, A:Y.127, J:M.79 Hydrogen bonds: A:A.72, A:R.84, A:D.85, A:H.88, A:Y.127, J:T.75 Water bridges: A:K.81, A:K.81, A:R.84, A:H.88, J:S.57, J:T.75 Salt bridges: A:K.78, A:K.81, A:R.84 pi-Cation interactions: A:R.84 PEB.2: 12 residues within 4Å: Chain A: K.43, L.44, N.47, A.50, V.51, E.54, R.137, L.138, C.139, R.142, D.143, M.144 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:K.43, A:A.50, A:V.51, A:R.137 Hydrogen bonds: A:K.43, A:N.47 Water bridges: A:R.142, A:D.143 Salt bridges: A:R.142 PEB.4: 17 residues within 4Å: Chain B: N.47, C.50, D.54, S.57, G.58, C.61, E.62, R.129, I.133, A.136, Q.137, A.140, F.141, A.146, T.147, E.148, R.149 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:D.54, B:I.133, B:A.136, B:Q.137, B:A.140, B:A.146 Hydrogen bonds: B:D.54, B:Q.137, B:T.147, B:E.148 Water bridges: B:E.62, B:E.62, B:R.129, B:R.129 Salt bridges: B:R.129 PEB.5: 21 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, Y.92, R.108, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, S.127 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:R.78, B:A.81, B:I.88, B:Y.92, B:L.113, B:T.116, B:L.120, B:V.122, B:V.122 Hydrogen bonds: B:D.85 Water bridges: B:R.84, B:R.84 Salt bridges: B:R.77, B:R.78, B:R.84 PEB.6: 18 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, T.143, N.144, F.153, A.154, A.155, G.156, C.158 Chain C: R.33, Q.147 23 PLIP interactions: 19 interactions with chain B, 3 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: B:N.35, B:K.36, B:L.38, B:D.39, B:A.40, B:N.144, B:F.153, B:F.153, B:F.153, B:A.154, C:R.33, A:L.24 Hydrogen bonds: B:N.35, B:D.39, B:A.154, B:G.156, C:Q.147 Water bridges: B:N.35, B:N.35, B:K.36, B:K.36, B:A.154, C:R.33 PEB.7: 23 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 H: I.67, T.75, N.76, M.79 25 PLIP interactions: 21 interactions with chain C, 4 interactions with chain H Hydrophobic interactions: C:A.72, C:K.78, C:K.81, C:K.81, C:H.88, C:Y.89, C:V.116, C:Y.117, C:L.120, C:L.122, C:A.126, C:Y.127, C:Y.127, H:M.79 Hydrogen bonds: C:A.72, C:R.84, C:D.85, H:S.57, H:T.75 Water bridges: C:K.81, C:K.81, H:T.75 Salt bridges: C:K.78, C:K.81, C:R.84 PEB.8: 11 residues within 4Å: Chain C: K.43, L.44, N.47, A.50, V.51, E.54, R.137, C.139, R.142, D.143, M.144 14 PLIP interactions: 14 interactions with chain C Hydrophobic interactions: C:K.43, C:A.50, C:V.51, C:R.137 Hydrogen bonds: C:K.43, C:N.47, C:R.142, C:R.142 Water bridges: C:D.143, C:D.143, C:D.143, C:D.143 Salt bridges: C:R.137, C:R.142 PEB.9: 18 residues within 4Å: Chain D: N.47, C.50, D.54, S.57, G.58, C.61, E.62, R.129, I.133, A.136, Q.137, A.140, F.141, T.145, A.146, T.147, E.148, R.149 16 PLIP interactions: 16 interactions with chain D Hydrophobic interactions: D:D.54, D:I.133, D:Q.137, D:A.140, D:A.146 Hydrogen bonds: D:D.54, D:Q.137, D:T.147 Water bridges: D:E.62, D:R.129, D:R.129, D:A.136, D:E.148, D:E.148 Salt bridges: D:R.129 pi-Stacking: D:F.141 PEB.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, S.127 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:R.78, D:A.81, D:I.88, D:L.113, D:L.120, D:V.122 Hydrogen bonds: D:D.85 Water bridges: D:R.77, D:R.77, D:R.84, D:R.84 Salt bridges: D:R.77, D:R.78, D:R.84 PEB.11: 19 residues within 4Å: Chain A: R.33, Q.147 Chain C: L.24, E.25, Q.28 Chain D: A.32, N.35, K.36, L.38, D.39, A.40, I.142, T.143, N.144, F.153, A.154, A.155, G.156, C.158 21 PLIP interactions: 17 interactions with chain D, 2 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: D:N.35, D:K.36, D:L.38, D:L.38, D:D.39, D:N.144, D:F.153, D:F.153, D:A.154, A:R.33, C:L.24 Hydrogen bonds: D:N.35, D:D.39, D:D.39, D:A.154, D:G.156, A:Q.147, C:Q.28 Water bridges: D:K.36, D:K.36, D:A.154 PEB.13: 23 residues within 4Å: Chain B: I.67, T.75, N.76, M.79 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 30 PLIP interactions: 4 interactions with chain B, 26 interactions with chain E Hydrophobic interactions: B:M.79, E:L.66, E:A.72, E:K.78, E:K.81, E:K.81, E:D.85, E:H.88, E:Y.89, E:V.116, E:L.120, E:A.126, E:Y.127, E:Y.127 Hydrogen bonds: B:T.75, E:A.72, E:R.84, E:D.85, E:H.88, E:Y.127 Water bridges: B:S.57, B:T.75, E:K.81, E:K.81, E:R.84, E:H.88 Salt bridges: E:K.78, E:K.81, E:R.84 pi-Cation interactions: E:R.84 PEB.14: 12 residues within 4Å: Chain E: K.43, L.44, N.47, A.50, V.51, E.54, R.137, L.138, C.139, R.142, D.143, M.144 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:K.43, E:A.50, E:V.51, E:R.137 Hydrogen bonds: E:K.43, E:N.47 Water bridges: E:R.142, E:D.143 Salt bridges: E:R.142 PEB.16: 17 residues within 4Å: Chain F: N.47, C.50, D.54, S.57, G.58, C.61, E.62, R.129, I.133, A.136, Q.137, A.140, F.141, A.146, T.147, E.148, R.149 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:D.54, F:I.133, F:A.136, F:Q.137, F:A.140, F:A.146 Hydrogen bonds: F:D.54, F:Q.137, F:T.147, F:E.148 Water bridges: F:E.62, F:E.62, F:R.129, F:R.129 Salt bridges: F:R.129 PEB.17: 21 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, Y.92, R.108, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, S.127 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:R.78, F:A.81, F:I.88, F:Y.92, F:L.113, F:T.116, F:L.120, F:V.122, F:V.122 Hydrogen bonds: F:D.85 Water bridges: F:R.84, F:R.84 Salt bridges: F:R.77, F:R.78, F:R.84 PEB.18: 18 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, T.143, N.144, F.153, A.154, A.155, G.156, C.158 Chain G: R.33, Q.147 23 PLIP interactions: 1 interactions with chain E, 19 interactions with chain F, 3 interactions with chain G Hydrophobic interactions: E:L.24, F:N.35, F:K.36, F:L.38, F:D.39, F:A.40, F:N.144, F:F.153, F:F.153, F:F.153, F:A.154, G:R.33 Hydrogen bonds: F:N.35, F:D.39, F:A.154, F:G.156, G:Q.147 Water bridges: F:N.35, F:N.35, F:K.36, F:K.36, F:A.154, G:R.33 PEB.19: 23 residues within 4Å: 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 Chain L: I.67, T.75, N.76, M.79 25 PLIP interactions: 21 interactions with chain G, 4 interactions with chain L Hydrophobic interactions: G:A.72, G:K.78, G:K.81, G:K.81, G:H.88, G:Y.89, G:V.116, G:Y.117, G:L.120, G:L.122, G:A.126, G:Y.127, G:Y.127, L:M.79 Hydrogen bonds: G:A.72, G:R.84, G:D.85, L:S.57, L:T.75 Water bridges: G:K.81, G:K.81, L:T.75 Salt bridges: G:K.78, G:K.81, G:R.84 PEB.20: 11 residues within 4Å: Chain G: K.43, L.44, N.47, A.50, V.51, E.54, R.137, C.139, R.142, D.143, M.144 14 PLIP interactions: 14 interactions with chain G Hydrophobic interactions: G:K.43, G:A.50, G:V.51, G:R.137 Hydrogen bonds: G:K.43, G:N.47, G:R.142, G:R.142 Water bridges: G:D.143, G:D.143, G:D.143, G:D.143 Salt bridges: G:R.137, G:R.142 PEB.21: 18 residues within 4Å: Chain H: N.47, C.50, D.54, S.57, G.58, C.61, E.62, R.129, I.133, A.136, Q.137, A.140, F.141, T.145, A.146, T.147, E.148, R.149 16 PLIP interactions: 16 interactions with chain H Hydrophobic interactions: H:D.54, H:I.133, H:Q.137, H:A.140, H:A.146 Hydrogen bonds: H:D.54, H:Q.137, H:T.147 Water bridges: H:E.62, H:R.129, H:R.129, H:A.136, H:E.148, H:E.148 Salt bridges: H:R.129 pi-Stacking: H:F.141 PEB.22: 19 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, L.113, Y.117, L.120, V.122, P.123, S.126, S.127 14 PLIP interactions: 14 interactions with chain H Hydrophobic interactions: H:R.78, H:A.81, H:I.88, H:L.113, H:L.120, H:V.122 Hydrogen bonds: H:D.85 Water bridges: H:R.77, H:R.77, H:R.84, H:R.84 Salt bridges: H:R.77, H:R.78, H:R.84 PEB.23: 19 residues within 4Å: Chain E: R.33, Q.147 Chain G: L.24, E.25, Q.28 Chain H: A.32, N.35, K.36, L.38, D.39, A.40, I.142, T.143, N.144, F.153, A.154, A.155, G.156, C.158 21 PLIP interactions: 2 interactions with chain G, 17 interactions with chain H, 2 interactions with chain E Hydrophobic interactions: G:L.24, H:N.35, H:K.36, H:L.38, H:L.38, H:D.39, H:N.144, H:F.153, H:F.153, H:A.154, E:R.33 Hydrogen bonds: G:Q.28, H:N.35, H:D.39, H:D.39, H:A.154, H:G.156, E:Q.147 Water bridges: H:K.36, H:K.36, H:A.154 PEB.25: 23 residues within 4Å: Chain F: I.67, 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 30 PLIP interactions: 26 interactions with chain I, 4 interactions with chain F Hydrophobic interactions: I:L.66, I:A.72, I:K.78, I:K.81, I:K.81, I:D.85, I:H.88, I:Y.89, I:V.116, I:L.120, I:A.126, I:Y.127, I:Y.127, F:M.79 Hydrogen bonds: I:A.72, I:R.84, I:D.85, I:H.88, I:Y.127, F:T.75 Water bridges: I:K.81, I:K.81, I:R.84, I:H.88, F:S.57, F:T.75 Salt bridges: I:K.78, I:K.81, I:R.84 pi-Cation interactions: I:R.84 PEB.26: 12 residues within 4Å: Chain I: K.43, L.44, N.47, A.50, V.51, E.54, R.137, L.138, C.139, R.142, D.143, M.144 9 PLIP interactions: 9 interactions with chain I Hydrophobic interactions: I:K.43, I:A.50, I:V.51, I:R.137 Hydrogen bonds: I:K.43, I:N.47 Water bridges: I:R.142, I:D.143 Salt bridges: I:R.142 PEB.28: 17 residues within 4Å: Chain J: N.47, C.50, D.54, S.57, G.58, C.61, E.62, R.129, I.133, A.136, Q.137, A.140, F.141, A.146, T.147, E.148, R.149 15 PLIP interactions: 15 interactions with chain J Hydrophobic interactions: J:D.54, J:I.133, J:A.136, J:Q.137, J:A.140, J:A.146 Hydrogen bonds: J:D.54, J:Q.137, J:T.147, J:E.148 Water bridges: J:E.62, J:E.62, J:R.129, J:R.129 Salt bridges: J:R.129 PEB.29: 21 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, Y.92, R.108, L.113, T.116, Y.117, L.120, V.122, P.123, S.126, S.127 15 PLIP interactions: 15 interactions with chain J Hydrophobic interactions: J:R.78, J:A.81, J:I.88, J:Y.92, J:L.113, J:T.116, J:L.120, J:V.122, J:V.122 Hydrogen bonds: J:D.85 Water bridges: J:R.84, J:R.84 Salt bridges: J:R.77, J:R.78, J:R.84 PEB.30: 18 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, T.143, N.144, F.153, A.154, A.155, G.156, C.158 Chain K: R.33, Q.147 23 PLIP interactions: 19 interactions with chain J, 1 interactions with chain I, 3 interactions with chain K Hydrophobic interactions: J:N.35, J:K.36, J:L.38, J:D.39, J:A.40, J:N.144, J:F.153, J:F.153, J:F.153, J:A.154, I:L.24, K:R.33 Hydrogen bonds: J:N.35, J:D.39, J:A.154, J:G.156, K:Q.147 Water bridges: J:N.35, J:N.35, J:K.36, J:K.36, J:A.154, K:R.33 PEB.31: 23 residues within 4Å: Chain D: I.67, 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 25 PLIP interactions: 4 interactions with chain D, 21 interactions with chain K Hydrophobic interactions: D:M.79, K:A.72, K:K.78, K:K.81, K:K.81, K:H.88, K:Y.89, K:V.116, K:Y.117, K:L.120, K:L.122, K:A.126, K:Y.127, K:Y.127 Hydrogen bonds: D:S.57, D:T.75, K:A.72, K:R.84, K:D.85 Water bridges: D:T.75, K:K.81, K:K.81 Salt bridges: K:K.78, K:K.81, K:R.84 PEB.32: 11 residues within 4Å: Chain K: K.43, L.44, N.47, A.50, V.51, E.54, R.137, C.139, R.142, D.143, M.144 14 PLIP interactions: 14 interactions with chain K Hydrophobic interactions: K:K.43, K:A.50, K:V.51, K:R.137 Hydrogen bonds: K:K.43, K:N.47, K:R.142, K:R.142 Water bridges: K:D.143, K:D.143, K:D.143, K:D.143 Salt bridges: K:R.137, K:R.142 PEB.33: 18 residues within 4Å: Chain L: N.47, C.50, D.54, S.57, G.58, C.61, E.62, R.129, I.133, A.136, Q.137, A.140, F.141, T.145, A.146, T.147, E.148, R.149 16 PLIP interactions: 16 interactions with chain L Hydrophobic interactions: L:D.54, L:I.133, L:Q.137, L:A.140, L:A.146 Hydrogen bonds: L:D.54, L:Q.137, L:T.147 Water bridges: L:E.62, L:R.129, L:R.129, L:A.136, L:E.148, L:E.148 Salt bridges: L:R.129 pi-Stacking: L:F.141 PEB.34: 19 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, L.113, Y.117, L.120, V.122, P.123, S.126, S.127 14 PLIP interactions: 14 interactions with chain L Hydrophobic interactions: L:R.78, L:A.81, L:I.88, L:L.113, L:L.120, L:V.122 Hydrogen bonds: L:D.85 Water bridges: L:R.77, L:R.77, L:R.84, L:R.84 Salt bridges: L:R.77, L:R.78, L:R.84 PEB.35: 19 residues within 4Å: Chain I: R.33, Q.147 Chain K: L.24, E.25, Q.28 Chain L: A.32, N.35, K.36, L.38, D.39, A.40, I.142, T.143, N.144, F.153, A.154, A.155, G.156, C.158 21 PLIP interactions: 17 interactions with chain L, 2 interactions with chain K, 2 interactions with chain I Hydrophobic interactions: L:N.35, L:K.36, L:L.38, L:L.38, L:D.39, L:N.144, L:F.153, L:F.153, L:A.154, K:L.24, I:R.33 Hydrogen bonds: L:N.35, L:D.39, L:D.39, L:A.154, L:G.156, K:Q.28, I:Q.147 Water bridges: L:K.36, L:K.36, L:A.154

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

SO4.3: 5 residues within 4Å: Chain A: L.122, P.123, T.124 Chain K: P.123, T.124 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain K Hydrogen bonds: A:T.124, A:T.124, K:T.124, K:T.124 Water bridges: A:S.125, A:S.125, K:S.125, K:S.125 SO4.12: 3 residues within 4Å: Chain D: M.1, D.107, R.108 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:M.1, D:M.1 Salt bridges: D:R.108 SO4.15: 5 residues within 4Å: Chain C: P.123, T.124 Chain E: L.122, P.123, T.124 8 PLIP interactions: 4 interactions with chain E, 4 interactions with chain C Hydrogen bonds: E:T.124, E:T.124, C:T.124, C:T.124 Water bridges: E:S.125, E:S.125, C:S.125, C:S.125 SO4.24: 3 residues within 4Å: Chain H: M.1, D.107, R.108 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:M.1, H:M.1 Salt bridges: H:R.108 SO4.27: 5 residues within 4Å: Chain G: P.123, T.124 Chain I: L.122, P.123, T.124 8 PLIP interactions: 4 interactions with chain I, 4 interactions with chain G Hydrogen bonds: I:T.124, I:T.124, G:T.124, G:T.124 Water bridges: I:S.125, I:S.125, G:S.125, G:S.125 SO4.36: 3 residues within 4Å: Chain L: M.1, D.107, R.108 3 PLIP interactions: 3 interactions with chain L Hydrogen bonds: L:M.1, L:M.1 Salt bridges: L:R.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liberti, D. et al., Inside out Porphyridium cruentum : Beyond the Conventional Biorefinery Concept. Acs Sustain Chem Eng (2023)

Release Date

2023-02-08

Peptides

B-phycoerythrin alpha chain: ACEGIK
B-phycoerythrin beta chain: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

C
CCC

E
AAA

G
CCC

I
AAA

K
CCC

B
BBB

D
DDD

F
BBB

H
DDD

J
BBB

L
DDD

B-phycoerythrin alpha chain

B-phycoerythrin beta chain

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