SMTL ID : 4l1e.1

Crystal structure of C-Phycocyanin from Leptolyngbya sp. N62DM

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.61 Å

Oligo State

hetero-6-6-mer

Ligands

5 x CYC: PHYCOCYANOBILIN(Non-covalent)

CYC.1: 33 residues within 4Å: Chain A: V.59, Y.60, T.66, P.72, N.73, Y.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, M.94, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129, A.132 Chain H: R.57, F.60, I.67, Y.74, T.75, S.76, M.79 23 PLIP interactions: 21 interactions with chain A, 2 interactions with chain H Hydrophobic interactions: A:T.66, A:K.83, A:K.83, A:Y.90, A:L.111, A:L.111, A:I.118, A:F.122, A:F.122, A:L.124, A:W.128, A:Y.129 Hydrogen bonds: A:N.73, A:A.75, A:R.86, A:Y.129, A:Y.129, H:T.75 Salt bridges: A:K.83, A:R.86, H:R.57 pi-Stacking: A:Y.90 pi-Cation interactions: A:R.86 CYC.4: 32 residues within 4Å: Chain C: V.59, Y.60, T.66, P.72, N.73, Y.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, M.94, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129 Chain L: R.57, F.60, I.67, Y.74, T.75, S.76, M.79 24 PLIP interactions: 21 interactions with chain C, 3 interactions with chain L Hydrophobic interactions: C:V.59, C:K.83, C:K.83, C:Y.90, C:L.111, C:I.118, C:F.122, C:F.122, C:W.128, C:W.128, C:Y.129, L:Y.74 Hydrogen bonds: C:N.73, C:A.75, C:R.86, C:D.87, L:T.75 Water bridges: C:R.86 Salt bridges: C:R.79, C:K.83, C:R.86, L:R.57 pi-Stacking: C:Y.90 pi-Cation interactions: C:R.86 CYC.7: 32 residues within 4Å: Chain D: R.57, F.60, I.67, Y.74, T.75, S.76, M.79 Chain E: V.59, Y.60, T.66, P.72, N.73, Y.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, M.94, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129 20 PLIP interactions: 17 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:V.59, E:K.83, E:Y.90, E:L.111, E:I.118, E:F.122, E:W.128, E:W.128, E:Y.129 Hydrogen bonds: E:N.73, E:R.86, E:D.87, E:Y.129, D:T.75 Salt bridges: E:R.79, E:K.83, E:R.86, D:R.57 pi-Cation interactions: E:R.86 Water bridges: D:R.57 CYC.10: 32 residues within 4Å: Chain G: V.59, Y.60, T.66, P.72, N.73, Y.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, M.94, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129 Chain J: R.57, F.60, I.67, Y.74, T.75, S.76, M.79 21 PLIP interactions: 3 interactions with chain J, 18 interactions with chain G Hydrophobic interactions: J:Y.74, G:V.59, G:K.83, G:K.83, G:L.111, G:L.111, G:I.118, G:F.122, G:W.128, G:W.128, G:Y.129 Hydrogen bonds: J:T.75, G:N.73, G:A.75, G:R.86, G:D.87 Salt bridges: J:R.57, G:R.79, G:K.83, G:R.86 pi-Cation interactions: G:R.86 CYC.16: 32 residues within 4Å: Chain F: R.57, F.60, I.67, Y.74, T.75, S.76, M.79 Chain K: V.59, Y.60, T.66, P.72, N.73, Y.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, M.94, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129 20 PLIP interactions: 18 interactions with chain K, 2 interactions with chain F Hydrophobic interactions: K:V.59, K:T.66, K:K.83, K:Y.90, K:I.118, K:I.118, K:F.122, K:W.128, K:W.128, K:Y.129 Hydrogen bonds: K:N.73, K:A.75, K:R.86, K:D.87, F:T.75 Salt bridges: K:R.79, K:K.83, K:R.86, F:R.57 pi-Cation interactions: K:R.86

13 x BLA: BILIVERDINE IX ALPHA(Non-covalent)

BLA.2: 23 residues within 4Å: Chain B: L.59, F.60, L.66, N.72, A.73, R.78, A.81, C.82, R.84, D.85, M.86, I.88, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, T.122, P.123, S.126, V.127 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.66, B:R.78, B:A.81, B:I.88, B:I.88, B:L.113, B:T.116, B:L.120, B:T.122, B:V.127 Hydrogen bonds: B:N.72, B:R.84, B:D.85 Salt bridges: B:R.84 pi-Cation interactions: B:R.84 BLA.3: 24 residues within 4Å: Chain A: S.21, I.24, F.28 Chain B: N.35, K.36, L.38, D.39, V.40, N.42, R.43, V.142, N.143, P.145, I.148, T.149, P.150, G.151, C.153, L.156 Chain C: R.32, Q.33, D.145, V.148, E.149 16 PLIP interactions: 11 interactions with chain B, 4 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: B:N.35, B:K.36, B:V.142, B:I.148, B:T.149, C:V.148 Hydrogen bonds: B:N.35, B:D.39, B:T.149, B:T.149, B:G.151, C:Q.33, C:D.145 Salt bridges: B:K.36 Water bridges: C:D.145 pi-Stacking: A:F.28 BLA.5: 23 residues within 4Å: Chain D: L.59, F.60, L.66, N.72, A.73, R.78, A.81, C.82, R.84, D.85, M.86, I.88, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, T.122, P.123, S.126, V.127 14 PLIP interactions: 14 interactions with chain D Hydrophobic interactions: D:L.59, D:L.66, D:R.78, D:A.81, D:I.88, D:I.88, D:T.116, D:L.120, D:V.127 Hydrogen bonds: D:N.72, D:R.84, D:D.85 Salt bridges: D:R.84 pi-Cation interactions: D:R.84 BLA.6: 25 residues within 4Å: Chain A: R.32, Q.33, D.145, V.148, E.149 Chain C: S.21, I.24, F.28 Chain D: E.33, N.35, K.36, L.38, D.39, V.40, N.42, R.43, V.142, N.143, P.145, I.148, T.149, P.150, G.151, C.153, L.156 20 PLIP interactions: 13 interactions with chain D, 6 interactions with chain A, 1 interactions with chain C Hydrophobic interactions: D:N.35, D:K.36, D:V.142, D:I.148, D:T.149, A:V.148 Hydrogen bonds: D:N.35, D:D.39, D:D.39, D:T.149, D:T.149, D:G.151, A:Q.33, A:D.145, A:D.145 Water bridges: D:A.32, A:D.145, A:D.145 Salt bridges: D:K.36 pi-Stacking: C:F.28 BLA.8: 23 residues within 4Å: Chain F: L.59, F.60, L.66, N.72, A.73, R.78, A.81, C.82, R.84, D.85, M.86, I.88, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, T.122, P.123, S.126, V.127 13 PLIP interactions: 13 interactions with chain F Hydrophobic interactions: F:L.66, F:R.78, F:A.81, F:T.116, F:L.120, F:T.122, F:V.127 Hydrogen bonds: F:N.72, F:R.84, F:R.84, F:D.85 Salt bridges: F:R.84 pi-Cation interactions: F:R.84 BLA.9: 26 residues within 4Å: Chain E: S.21, I.24, F.28 Chain F: E.33, N.35, K.36, L.38, D.39, V.40, N.42, R.43, V.142, N.143, D.144, P.145, I.148, T.149, P.150, G.151, C.153, L.156 Chain G: R.32, Q.33, D.145, V.148, E.149 17 PLIP interactions: 10 interactions with chain F, 2 interactions with chain E, 5 interactions with chain G Hydrophobic interactions: F:N.35, F:K.36, F:V.142, F:I.148, F:T.149, E:I.24, G:V.148 Hydrogen bonds: F:N.35, F:D.39, F:T.149, F:T.149, F:G.151, G:Q.33, G:D.145, G:D.145, G:D.145 pi-Stacking: E:F.28 BLA.11: 23 residues within 4Å: Chain H: L.59, F.60, L.66, N.72, A.73, R.78, A.81, C.82, R.84, D.85, M.86, I.88, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, T.122, P.123, S.126, V.127 15 PLIP interactions: 15 interactions with chain H Hydrophobic interactions: H:R.78, H:R.78, H:A.81, H:I.88, H:I.88, H:T.116, H:L.120, H:T.122, H:V.127 Hydrogen bonds: H:N.72, H:R.84, H:D.85 Salt bridges: H:R.78, H:R.84 pi-Cation interactions: H:R.84 BLA.12: 26 residues within 4Å: Chain E: R.32, Q.33, D.145, V.148, E.149 Chain G: S.21, I.24, F.28 Chain H: E.33, N.35, K.36, L.38, D.39, V.40, N.42, R.43, V.142, N.143, D.144, P.145, I.148, T.149, P.150, G.151, C.153, L.156 17 PLIP interactions: 3 interactions with chain E, 12 interactions with chain H, 2 interactions with chain G Hydrophobic interactions: E:V.148, H:N.35, H:K.36, H:K.36, H:I.148, H:T.149, G:I.24 Hydrogen bonds: E:Q.33, E:D.145, H:N.35, H:D.39, H:T.149, H:T.149, H:G.151 Water bridges: H:T.149, H:T.149 pi-Stacking: G:F.28 BLA.13: 32 residues within 4Å: Chain B: R.57, F.60, I.67, Y.74, T.75, S.76, M.79 Chain I: V.59, Y.60, T.66, P.72, N.73, Y.74, A.75, R.79, G.80, K.83, C.84, R.86, D.87, I.88, Y.90, Y.91, M.94, Y.110, L.111, I.115, I.118, F.122, L.124, W.128, Y.129 24 PLIP interactions: 22 interactions with chain I, 2 interactions with chain B Hydrophobic interactions: I:V.59, I:T.66, I:K.83, I:K.83, I:Y.90, I:L.111, I:I.115, I:I.118, I:F.122, I:F.122, I:W.128, I:W.128, I:Y.129 Hydrogen bonds: I:N.73, I:A.75, I:R.86, I:D.87, B:T.75 Water bridges: I:R.86 Salt bridges: I:R.79, I:K.83, I:R.86, B:R.57 pi-Cation interactions: I:R.86 BLA.14: 23 residues within 4Å: Chain J: L.59, F.60, L.66, N.72, A.73, R.78, A.81, C.82, R.84, D.85, M.86, I.88, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, T.122, P.123, S.126, V.127 12 PLIP interactions: 12 interactions with chain J Hydrophobic interactions: J:L.59, J:R.78, J:A.81, J:I.88, J:T.116, J:L.120, J:V.127 Hydrogen bonds: J:N.72, J:R.84, J:D.85 Salt bridges: J:R.84 pi-Cation interactions: J:R.84 BLA.15: 26 residues within 4Å: Chain I: S.21, I.24, Q.25, F.28 Chain J: N.35, K.36, L.38, D.39, V.40, N.42, R.43, V.142, N.143, D.144, P.145, I.148, T.149, P.150, G.151, C.153, L.156 Chain K: R.32, Q.33, D.145, V.148, E.149 17 PLIP interactions: 3 interactions with chain K, 2 interactions with chain I, 12 interactions with chain J Hydrophobic interactions: K:V.148, I:F.28, J:N.35, J:K.36, J:K.36, J:V.142, J:I.148, J:T.149 Hydrogen bonds: K:Q.33, K:D.145, J:N.35, J:D.39, J:T.149, J:T.149, J:G.151 pi-Stacking: I:F.28 Salt bridges: J:K.36 BLA.17: 23 residues within 4Å: Chain L: L.59, F.60, L.66, N.72, A.73, R.78, A.81, C.82, R.84, D.85, M.86, I.88, Y.92, R.108, C.109, L.113, T.116, Y.117, L.120, T.122, P.123, S.126, V.127 13 PLIP interactions: 13 interactions with chain L Hydrophobic interactions: L:L.59, L:L.66, L:R.78, L:R.78, L:A.81, L:I.88, L:L.120, L:V.127 Hydrogen bonds: L:N.72, L:R.84, L:D.85 Salt bridges: L:R.84 pi-Cation interactions: L:R.84 BLA.18: 25 residues within 4Å: Chain I: R.32, Q.33, D.145, V.148, E.149 Chain K: S.21, I.24, F.28 Chain L: N.35, K.36, L.38, D.39, V.40, N.42, R.43, V.142, N.143, D.144, P.145, I.148, T.149, P.150, G.151, C.153, L.156 16 PLIP interactions: 9 interactions with chain L, 5 interactions with chain I, 2 interactions with chain K Hydrophobic interactions: L:N.35, L:K.36, L:V.40, L:I.148, L:T.149, I:V.148, K:F.28 Hydrogen bonds: L:N.35, L:D.39, L:T.149, L:G.151, I:Q.33, I:D.145 Water bridges: I:D.145, I:D.145 pi-Stacking: K:F.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, N.K. et al., Crystal Structure and Interaction of Phycocyanin with beta-Secretase: A Putative Therapy for Alzheimer's Disease. CNS Neurol Disord Drug Targets (2014)

Release Date

2014-05-21

Peptides

Phycocyanin alpha chain: ACEGIK
Phycocyanin beta chain: BDFHJL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
C

E
E

G
G

I
I

K
K

B
B

D
D

F
F

H
H

J
J

L
L

Phycocyanin alpha chain

Phycocyanin beta chain

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