eF-site ID 2ziy-A
PDB Code 2ziy
Chain A

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Title Crystal structure of squid rhodopsin
Classification SIGNALING PROTEIN
Compound Rhodopsin
Source ORGANISM_COMMON: Japanese flying squid; ORGANISM_SCIENTIFIC: Todarodes pacificus;
Sequence A:  DLRDNETWWYNPSIIVHPHWREFDQVPDAVYYSLGIFIGI
CGIIGCGGNGIVIYLFTKTKSLQTPANMFIINLAFSDFTF
SLVNGFPLMTISCFLKKWIFGFAACKVYGFIGGIFGFMSI
MTMAMISIDRYNVIGRPMAASKKMSHRRAFIMIIFVWLWS
VLWAIGPIFGWGAYTLEGVLCNCSFDYISRDSTTRSNILC
MFILGFFGPILIIFFCYFNIVMSVSNHEKEMAAMAKRLNA
KELRKAQAGANAEMRLAKISIVIVSQFLLSWSPYAVVALL
AQFGPLEWVTPYAAQLPVMFAKASAIHNPMIYSVSHPKFR
EAISQTFPWVLTCCQFDDKETEDDKDAETEIPAGESSDAA
PSADAAQMKE
Description (1)  Rhodopsin


Functional site

1) chain A
residue 120
type
ligand
sequence F
description BINDING SITE FOR RESIDUE RET A 380
source : AC1

2) chain A
residue 186
type
ligand
sequence C
description BINDING SITE FOR RESIDUE RET A 380
source : AC1

3) chain A
residue 204
type
ligand
sequence M
description BINDING SITE FOR RESIDUE RET A 380
source : AC1

4) chain A
residue 209
type
ligand
sequence F
description BINDING SITE FOR RESIDUE RET A 380
source : AC1

5) chain A
residue 274
type
ligand
sequence W
description BINDING SITE FOR RESIDUE RET A 380
source : AC1

6) chain A
residue 305
type
ligand
sequence K
description BINDING SITE FOR RESIDUE RET A 380
source : AC1

7) chain A
residue 336
type
ligand
sequence C
description BINDING SITE FOR RESIDUE PLM A 381
source : AC2

8) chain A
residue 316
type
ligand
sequence S
description BINDING SITE FOR RESIDUE PLM A 382
source : AC3

9) chain A
residue 336
type
ligand
sequence C
description BINDING SITE FOR RESIDUE PLM A 382
source : AC3

10) chain A
residue 337
type
ligand
sequence C
description BINDING SITE FOR RESIDUE PLM A 382
source : AC3

11) chain A
residue 199-226
type TRANSMEM
ligand
sequence SNILCMFILGFFGPILIIFFCYFNIVMS
description Helical; Name=5; (Potential).
source Swiss-Prot : SWS_FT_FI1

12) chain A
residue 70-96
type TRANSMEM
ligand
sequence NMFIINLAFSDFTFSLVNGFPLMTISC
description Helical; Name=2; (Potential).
source Swiss-Prot : SWS_FT_FI2

13) chain A
residue 293-317
type TRANSMEM
ligand
sequence TPYAAQLPVMFAKASAIHNPMIYSV
description Helical; Name=7; (Potential).
source Swiss-Prot : SWS_FT_FI3

14) chain A
residue 151-174
type TRANSMEM
ligand
sequence RAFIMIIFVWLWSVLWAIGPIFGW
description Helical; Name=4; (Potential).
source Swiss-Prot : SWS_FT_FI4

15) chain A
residue 33-57
type TRANSMEM
ligand
sequence VYYSLGIFIGICGIIGCGGNGIVIY
description Helical; Name=1; (Potential).
source Swiss-Prot : SWS_FT_FI5

16) chain A
residue 261-284
type TRANSMEM
ligand
sequence KISIVIVSQFLLSWSPYAVVALLA
description Helical; Name=6; (Potential).
source Swiss-Prot : SWS_FT_FI6

17) chain A
residue 111-130
type TRANSMEM
ligand
sequence YGFIGGIFGFMSIMTMAMIS
description Helical; Name=3; (Potential).
source Swiss-Prot : SWS_FT_FI7

18) chain A
residue 121-137
type prosite
ligand
sequence MSIMTMAMISIDRYNVI
description G-protein coupled receptors family 1 signature. [GSTALIVMFYWC]-[GSTANCPDE]-{EDPKRH}-x-{PQ}-[LIVMNQGA]-{RK}-{RK}-[LIVMFT]
source prosite : PS00237

19) chain A
residue 299-315
type prosite
ligand
sequence LPVMFAKASAIHNPMIY
description Visual pigments (opsins) retinal binding site. [LIVMFWAC]-[PSGAC]-x-{G}-x-[SAC]-K-[STALIMR]-[GSACPNV]-[STACP]-x(2)
source prosite : PS00238

20) chain A
residue 43
type binding
ligand PLM: PALMITIC ACID
sequence I
description PALMITIC ACID binding site
source pdb_hetatom : PLM_2ziy_A_381

21) chain A
residue 336
type binding
ligand PLM: PALMITIC ACID
sequence C
description PALMITIC ACID binding site
source pdb_hetatom : PLM_2ziy_A_381

22) chain A
residue 87
type binding
ligand RET: RETINAL
sequence N
description RETINAL binding site
source pdb_hetatom : RET_2ziy_A_380

23) chain A
residue 111-112
type binding
ligand RET: RETINAL
sequence YG
description RETINAL binding site
source pdb_hetatom : RET_2ziy_A_380

24) chain A
residue 115-116
type binding
ligand RET: RETINAL
sequence GG
description RETINAL binding site
source pdb_hetatom : RET_2ziy_A_380

25) chain A
residue 120
type binding
ligand RET: RETINAL
sequence F
description RETINAL binding site
source pdb_hetatom : RET_2ziy_A_380

26) chain A
residue 177
type binding
ligand RET: RETINAL
sequence Y
description RETINAL binding site
source pdb_hetatom : RET_2ziy_A_380

27) chain A
residue 185-188
type binding
ligand RET: RETINAL
sequence NCSF
description RETINAL binding site
source pdb_hetatom : RET_2ziy_A_380

28) chain A
residue 204-205
type binding
ligand RET: RETINAL
sequence MF
description RETINAL binding site
source pdb_hetatom : RET_2ziy_A_380

29) chain A
residue 208-209
type binding
ligand RET: RETINAL
sequence GF
description RETINAL binding site
source pdb_hetatom : RET_2ziy_A_380

30) chain A
residue 274
type binding
ligand RET: RETINAL
sequence W
description RETINAL binding site
source pdb_hetatom : RET_2ziy_A_380

31) chain A
residue 277-278
type binding
ligand RET: RETINAL
sequence YA
description RETINAL binding site
source pdb_hetatom : RET_2ziy_A_380

32) chain A
residue 301
type binding
ligand RET: RETINAL
sequence V
description RETINAL binding site
source pdb_hetatom : RET_2ziy_A_380

33) chain A
residue 305
type binding
ligand RET: RETINAL
sequence K
description RETINAL binding site
source pdb_hetatom : RET_2ziy_A_380

34) chain A
residue 313
type binding
ligand PLM: PALMITIC ACID
sequence M
description PALMITIC ACID binding site
source pdb_hetatom : PLM_2ziy_A_382

35) chain A
residue 316-317
type binding
ligand PLM: PALMITIC ACID
sequence SV
description PALMITIC ACID binding site
source pdb_hetatom : PLM_2ziy_A_382

36) chain A
residue 333-337
type binding
ligand PLM: PALMITIC ACID
sequence VLTCC
description PALMITIC ACID binding site
source pdb_hetatom : PLM_2ziy_A_382


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