SMTL ID : 1b8d.1

CRYSTAL STRUCTURE OF A PHYCOUROBILIN-CONTAINING PHYCOERYTHRIN

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-6-6-mer

Ligands

3 x GLY- TYR- UNK- TYR- UNK: PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (GAMMA CHAIN))(Non-covalent)

GLY-TYR-UNK-TYR-UNK.1: 12 residues within 4Å: Chain B: C.109, N.111, G.112, L.113, T.116 Chain D: C.109, N.111, G.112, L.113, T.116 Ligands: PEB.4, PEB.9 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:C.109, B:T.116 GLY-TYR-UNK-TYR-UNK.12: 12 residues within 4Å: Chain F: C.109, N.111, G.112, L.113, T.116 Chain H: C.109, N.111, G.112, L.113, T.116 Ligands: PEB.15, PEB.20 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:C.109, F:T.116 GLY-TYR-UNK-TYR-UNK.23: 12 residues within 4Å: Chain J: C.109, N.111, G.112, L.113, T.116 Chain L: C.109, N.111, G.112, L.113, T.116 Ligands: PEB.26, PEB.31 2 PLIP interactions: 2 interactions with chain J Hydrogen bonds: J:C.109, J:T.116

24 x PEB: PHYCOERYTHROBILIN(Covalent)

PEB.2: 24 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.67, Y.74, T.75, N.76, M.79 27 PLIP interactions: 24 interactions with chain A, 3 interactions with chain F Hydrophobic interactions: A:A.72, A:K.78, A:K.81, A:K.81, A:Y.89, A:V.116, A:L.120, A:L.122, A:A.126, A:Y.127, F:I.67, F:M.79 Hydrogen bonds: A:K.78, A:R.84, A:D.85, A:D.85, A:H.88, F:T.75 Water bridges: A:K.81, A:K.81, A:K.81, A:K.81 Salt bridges: A:K.78, A:K.81, A:R.84 pi-Cation interactions: A:R.84, A:H.88 PEB.3: 14 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, F.152 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:A.50, A:V.51, A:R.137, A:F.152 Hydrogen bonds: A:N.47, A:R.142, A:D.143 Water bridges: A:D.143, A:D.143, A:D.143 Salt bridges: A:R.137, A:R.142 pi-Cation interactions: A:R.142 PEB.4: 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, R.108, L.113, Y.117, L.120, V.122, P.123, S.126, S.127, A.130 Ligands: GLY-TYR-UNK-TYR-UNK.1 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:R.78, B:A.81, B:I.88, B:L.113, B:L.120, B:V.122, B:A.130 Hydrogen bonds: B:R.84, B:D.85, B:D.85, B:D.85 Salt bridges: B:R.77, B:R.78, B:R.84 pi-Cation interactions: B:R.84 PEB.5: 20 residues within 4Å: Chain A: L.24, E.25, Q.28 Chain B: N.35, K.36, L.38, D.39, A.40, N.42, I.142, T.143, N.144, V.153, A.154, A.155, G.156, C.158 Chain C: R.33, S.146, Q.147 22 PLIP interactions: 2 interactions with chain A, 17 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: A:L.24, B:N.35, B:K.36, B:L.38, B:L.38, B:N.144, B:V.153, B:V.153, B:A.154 Hydrogen bonds: A:Q.28, B:N.35, B:D.39, B:D.39, B:D.39, B:A.154, B:G.156 Water bridges: B:N.35, B:K.36, B:K.36, C:Q.147, C:Q.147, C:Q.147 PEB.7: 24 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, 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 26 PLIP interactions: 22 interactions with chain C, 4 interactions with chain L Hydrophobic interactions: C:A.72, C:K.78, C:K.81, C:K.81, C:H.88, C:Y.89, C:L.120, C:L.122, C:P.123, C:A.126, C:Y.127, L:I.60, L:I.67, L:M.79 Hydrogen bonds: C:K.78, C:R.84, C:D.85, C:D.85, C:H.88, L:T.75 Water bridges: C:K.78, C:K.81 Salt bridges: C:K.78, C:K.81, C:R.84 pi-Cation interactions: C:R.84 PEB.8: 12 residues within 4Å: Chain C: N.47, A.50, V.51, E.54, T.134, R.137, L.138, C.139, R.142, D.143, M.144, F.152 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:A.50, C:V.51, C:R.137, C:L.138, C:F.152 Hydrogen bonds: C:N.47, C:R.142, C:D.143 Water bridges: C:D.143 Salt bridges: C:R.137, C:R.142 pi-Cation interactions: C:R.142 PEB.9: 21 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, Y.92, R.108, L.113, Y.117, L.120, V.122, P.123, S.126, S.127 Ligands: GLY-TYR-UNK-TYR-UNK.1 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:R.78, D:A.81, D:I.88, D:L.120, D:V.122 Hydrogen bonds: D:R.84, D:D.85, D:D.85, D:D.85 Water bridges: D:R.77 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, N.42, I.142, T.143, N.144, V.153, A.154, A.155, G.156, C.158 20 PLIP interactions: 17 interactions with chain D, 1 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: D:N.35, D:K.36, D:L.38, D:L.38, D:N.144, D:V.153, D:A.154, 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:N.35, D:N.35, D:N.35, D:N.35, D:A.154 PEB.13: 24 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.67, Y.74, T.75, N.76, M.79 27 PLIP interactions: 24 interactions with chain E, 3 interactions with chain J Hydrophobic interactions: E:A.72, E:K.78, E:K.81, E:K.81, E:Y.89, E:V.116, E:L.120, E:L.122, E:A.126, E:Y.127, J:I.67, J:M.79 Hydrogen bonds: E:K.78, E:R.84, E:D.85, E:D.85, E:H.88, J:T.75 Water bridges: E:K.81, E:K.81, E:K.81, E:K.81 Salt bridges: E:K.78, E:K.81, E:R.84 pi-Cation interactions: E:R.84, E:H.88 PEB.14: 14 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, F.152 13 PLIP interactions: 13 interactions with chain E Hydrophobic interactions: E:A.50, E:V.51, E:R.137, E:F.152 Hydrogen bonds: E:N.47, E:R.142, E:D.143 Water bridges: E:D.143, E:D.143, E:D.143 Salt bridges: E:R.137, E:R.142 pi-Cation interactions: E:R.142 PEB.15: 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, R.108, L.113, Y.117, L.120, V.122, P.123, S.126, S.127, A.130 Ligands: GLY-TYR-UNK-TYR-UNK.12 15 PLIP interactions: 15 interactions with chain F Hydrophobic interactions: F:R.78, F:A.81, F:I.88, F:L.113, F:L.120, F:V.122, F:A.130 Hydrogen bonds: F:R.84, F:D.85, F:D.85, F:D.85 Salt bridges: F:R.77, F:R.78, F:R.84 pi-Cation interactions: F:R.84 PEB.16: 20 residues within 4Å: Chain E: L.24, E.25, Q.28 Chain F: N.35, K.36, L.38, D.39, A.40, N.42, I.142, T.143, N.144, V.153, A.154, A.155, G.156, C.158 Chain G: R.33, S.146, Q.147 22 PLIP interactions: 3 interactions with chain G, 17 interactions with chain F, 2 interactions with chain E Water bridges: G:Q.147, G:Q.147, G:Q.147, F:N.35, F:K.36, F:K.36 Hydrophobic interactions: F:N.35, F:K.36, F:L.38, F:L.38, F:N.144, F:V.153, F:V.153, F:A.154, E:L.24 Hydrogen bonds: F:N.35, F:D.39, F:D.39, F:D.39, F:A.154, F:G.156, E:Q.28 PEB.18: 24 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, Y.117, L.120, L.122, P.123, A.126, Y.127 26 PLIP interactions: 22 interactions with chain G, 4 interactions with chain D Hydrophobic interactions: G:A.72, G:K.78, G:K.81, G:K.81, G:H.88, G:Y.89, G:L.120, G:L.122, G:P.123, G:A.126, G:Y.127, D:I.60, D:I.67, D:M.79 Hydrogen bonds: G:K.78, G:R.84, G:D.85, G:D.85, G:H.88, D:T.75 Water bridges: G:K.78, G:K.81 Salt bridges: G:K.78, G:K.81, G:R.84 pi-Cation interactions: G:R.84 PEB.19: 12 residues within 4Å: Chain G: N.47, A.50, V.51, E.54, T.134, R.137, L.138, C.139, R.142, D.143, M.144, F.152 12 PLIP interactions: 12 interactions with chain G Hydrophobic interactions: G:A.50, G:V.51, G:R.137, G:L.138, G:F.152 Hydrogen bonds: G:N.47, G:R.142, G:D.143 Water bridges: G:D.143 Salt bridges: G:R.137, G:R.142 pi-Cation interactions: G:R.142 PEB.20: 21 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, Y.92, R.108, L.113, Y.117, L.120, V.122, P.123, S.126, S.127 Ligands: GLY-TYR-UNK-TYR-UNK.12 14 PLIP interactions: 14 interactions with chain H Hydrophobic interactions: H:R.78, H:A.81, H:I.88, H:L.120, H:V.122 Hydrogen bonds: H:R.84, H:D.85, H:D.85, H:D.85 Water bridges: H:R.77 Salt bridges: H:R.77, H:R.78, H:R.84 pi-Cation interactions: H:R.84 PEB.21: 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, N.42, I.142, T.143, N.144, V.153, A.154, A.155, G.156, C.158 20 PLIP interactions: 17 interactions with chain H, 2 interactions with chain G, 1 interactions with chain E Hydrophobic interactions: H:N.35, H:K.36, H:L.38, H:L.38, H:N.144, H:V.153, H:A.154, G:L.24 Hydrogen bonds: H:N.35, H:D.39, H:D.39, H:A.154, H:G.156, G:Q.28, E:Q.147 Water bridges: H:N.35, H:N.35, H:N.35, H:N.35, H:A.154 PEB.24: 24 residues within 4Å: Chain B: 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 27 PLIP interactions: 24 interactions with chain I, 3 interactions with chain B Hydrophobic interactions: I:A.72, I:K.78, I:K.81, I:K.81, I:Y.89, I:V.116, I:L.120, I:L.122, I:A.126, I:Y.127, B:I.67, B:M.79 Hydrogen bonds: I:K.78, I:R.84, I:D.85, I:D.85, I:H.88, B:T.75 Water bridges: I:K.81, I:K.81, I:K.81, I:K.81 Salt bridges: I:K.78, I:K.81, I:R.84 pi-Cation interactions: I:R.84, I:H.88 PEB.25: 14 residues within 4Å: Chain I: 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, F.152 13 PLIP interactions: 13 interactions with chain I Hydrophobic interactions: I:A.50, I:V.51, I:R.137, I:F.152 Hydrogen bonds: I:N.47, I:R.142, I:D.143 Water bridges: I:D.143, I:D.143, I:D.143 Salt bridges: I:R.137, I:R.142 pi-Cation interactions: I:R.142 PEB.26: 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, R.108, L.113, Y.117, L.120, V.122, P.123, S.126, S.127, A.130 Ligands: GLY-TYR-UNK-TYR-UNK.23 15 PLIP interactions: 15 interactions with chain J Hydrophobic interactions: J:R.78, J:A.81, J:I.88, J:L.113, J:L.120, J:V.122, J:A.130 Hydrogen bonds: J:R.84, J:D.85, J:D.85, J:D.85 Salt bridges: J:R.77, J:R.78, J:R.84 pi-Cation interactions: J:R.84 PEB.27: 20 residues within 4Å: Chain I: L.24, E.25, Q.28 Chain J: N.35, K.36, L.38, D.39, A.40, N.42, I.142, T.143, N.144, V.153, A.154, A.155, G.156, C.158 Chain K: R.33, S.146, Q.147 22 PLIP interactions: 2 interactions with chain I, 17 interactions with chain J, 3 interactions with chain K Hydrophobic interactions: I:L.24, J:N.35, J:K.36, J:L.38, J:L.38, J:N.144, J:V.153, J:V.153, J:A.154 Hydrogen bonds: I:Q.28, J:N.35, J:D.39, J:D.39, J:D.39, J:A.154, J:G.156 Water bridges: J:N.35, J:K.36, J:K.36, K:Q.147, K:Q.147, K:Q.147 PEB.29: 24 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, Y.117, L.120, L.122, P.123, A.126, Y.127 26 PLIP interactions: 22 interactions with chain K, 4 interactions with chain H Hydrophobic interactions: K:A.72, K:K.78, K:K.81, K:K.81, K:H.88, K:Y.89, K:L.120, K:L.122, K:P.123, K:A.126, K:Y.127, H:I.60, H:I.67, H:M.79 Hydrogen bonds: K:K.78, K:R.84, K:D.85, K:D.85, K:H.88, H:T.75 Water bridges: K:K.78, K:K.81 Salt bridges: K:K.78, K:K.81, K:R.84 pi-Cation interactions: K:R.84 PEB.30: 12 residues within 4Å: Chain K: N.47, A.50, V.51, E.54, T.134, R.137, L.138, C.139, R.142, D.143, M.144, F.152 12 PLIP interactions: 12 interactions with chain K Hydrophobic interactions: K:A.50, K:V.51, K:R.137, K:L.138, K:F.152 Hydrogen bonds: K:N.47, K:R.142, K:D.143 Water bridges: K:D.143 Salt bridges: K:R.137, K:R.142 pi-Cation interactions: K:R.142 PEB.31: 21 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, Y.92, R.108, L.113, Y.117, L.120, V.122, P.123, S.126, S.127 Ligands: GLY-TYR-UNK-TYR-UNK.23 14 PLIP interactions: 14 interactions with chain L Hydrophobic interactions: L:R.78, L:A.81, L:I.88, L:L.120, L:V.122 Hydrogen bonds: L:R.84, L:D.85, L:D.85, L:D.85 Water bridges: L:R.77 Salt bridges: L:R.77, L:R.78, L:R.84 pi-Cation interactions: L:R.84 PEB.32: 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, N.42, I.142, T.143, N.144, V.153, A.154, A.155, G.156, C.158 20 PLIP interactions: 17 interactions with chain L, 2 interactions with chain K, 1 interactions with chain I Hydrophobic interactions: L:N.35, L:K.36, L:L.38, L:L.38, L:N.144, L:V.153, L:A.154, K:L.24 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:N.35, L:N.35, L:N.35, L:N.35, L:A.154

6 x PUB: PHYCOUROBILIN(Covalent)

PUB.6: 16 residues within 4Å: Chain B: C.50, D.54, S.57, G.58, C.61, E.62, R.129, I.133, A.136, T.137, A.140, T.145, A.146, S.147, G.148, R.149 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:I.133, B:T.137, B:A.146 Hydrogen bonds: B:D.54, B:S.147, B:G.148 Water bridges: B:A.136 Salt bridges: B:R.129 PUB.11: 16 residues within 4Å: Chain D: C.50, D.54, S.57, G.58, C.61, E.62, R.129, I.133, A.136, T.137, F.141, T.145, A.146, S.147, G.148, R.149 11 PLIP interactions: 11 interactions with chain D Hydrophobic interactions: D:I.133, D:I.133, D:A.136, D:T.137, D:F.141, D:A.146 Hydrogen bonds: D:D.54, D:S.147, D:G.148 Water bridges: D:A.136 Salt bridges: D:R.129 PUB.17: 16 residues within 4Å: Chain F: C.50, D.54, S.57, G.58, C.61, E.62, R.129, I.133, A.136, T.137, A.140, T.145, A.146, S.147, G.148, R.149 8 PLIP interactions: 8 interactions with chain F Hydrophobic interactions: F:I.133, F:T.137, F:A.146 Hydrogen bonds: F:D.54, F:S.147, F:G.148 Water bridges: F:A.136 Salt bridges: F:R.129 PUB.22: 16 residues within 4Å: Chain H: C.50, D.54, S.57, G.58, C.61, E.62, R.129, I.133, A.136, T.137, F.141, T.145, A.146, S.147, G.148, R.149 11 PLIP interactions: 11 interactions with chain H Hydrophobic interactions: H:I.133, H:I.133, H:A.136, H:T.137, H:F.141, H:A.146 Hydrogen bonds: H:D.54, H:S.147, H:G.148 Water bridges: H:A.136 Salt bridges: H:R.129 PUB.28: 16 residues within 4Å: Chain J: C.50, D.54, S.57, G.58, C.61, E.62, R.129, I.133, A.136, T.137, A.140, T.145, A.146, S.147, G.148, R.149 8 PLIP interactions: 8 interactions with chain J Hydrophobic interactions: J:I.133, J:T.137, J:A.146 Hydrogen bonds: J:D.54, J:S.147, J:G.148 Water bridges: J:A.136 Salt bridges: J:R.129 PUB.33: 16 residues within 4Å: Chain L: C.50, D.54, S.57, G.58, C.61, E.62, R.129, I.133, A.136, T.137, F.141, T.145, A.146, S.147, G.148, R.149 11 PLIP interactions: 11 interactions with chain L Hydrophobic interactions: L:I.133, L:I.133, L:A.136, L:T.137, L:F.141, L:A.146 Hydrogen bonds: L:D.54, L:S.147, L:G.148 Water bridges: L:A.136 Salt bridges: L:R.129

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ritter, S. et al., Crystal structure of a phycourobilin-containing phycoerythrin at 1.90-A resolution. J.Struct.Biol. (1999)

Release Date

1999-02-18

Peptides

PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (ALPHA CHAIN)): ACEGIK
PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (BETA CHAIN)): BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
K

E
A

G
K

I
A

K
K

B
B

D
L

F
B

H
L

J
B

L
L

PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (ALPHA CHAIN))

PROTEIN (RHODOPHYTAN PHYCOERYTHRIN (BETA CHAIN))