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


Functional site
1) chain A
residue 120
type
sequence F
description BINDING SITE FOR RESIDUE RET A 380
source : AC1
2) chain A
residue 186
type
sequence C
description BINDING SITE FOR RESIDUE RET A 380
source : AC1
3) chain A
residue 204
type
sequence M
description BINDING SITE FOR RESIDUE RET A 380
source : AC1
4) chain A
residue 209
type
sequence F
description BINDING SITE FOR RESIDUE RET A 380
source : AC1
5) chain A
residue 274
type
sequence W
description BINDING SITE FOR RESIDUE RET A 380
source : AC1
6) chain A
residue 305
type
sequence K
description BINDING SITE FOR RESIDUE RET A 380
source : AC1
7) chain A
residue 336
type
sequence C
description BINDING SITE FOR RESIDUE PLM A 381
source : AC2
8) chain A
residue 316
type
sequence S
description BINDING SITE FOR RESIDUE PLM A 382
source : AC3
9) chain A
residue 336
type
sequence C
description BINDING SITE FOR RESIDUE PLM A 382
source : AC3
10) chain A
residue 337
type
sequence C
description BINDING SITE FOR RESIDUE PLM A 382
source : AC3
11) chain A
residue 98-109
type TOPO_DOM
sequence LKKWIFGFAACK
description Extracellular => ECO:0000269|PubMed:18463093, ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602, ECO:0000269|PubMed:26024518
source Swiss-Prot : SWS_FT_FI1
12) chain A
residue 173-199
type TOPO_DOM
sequence GWGAYTLEGVLCNCSFDYISRDSTTRS
description Extracellular => ECO:0000269|PubMed:18463093, ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602, ECO:0000269|PubMed:26024518
source Swiss-Prot : SWS_FT_FI1
13) chain A
residue 284-293
type TOPO_DOM
sequence AQFGPLEWVT
description Extracellular => ECO:0000269|PubMed:18463093, ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602, ECO:0000269|PubMed:26024518
source Swiss-Prot : SWS_FT_FI1
14) chain A
residue 34-58
type TRANSMEM
sequence YYSLGIFIGICGIIGCGGNGIVIYL
description Helical; Name=1 => ECO:0000269|PubMed:18463093, ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602, ECO:0000269|PubMed:26024518
source Swiss-Prot : SWS_FT_FI2
15) chain A
residue 59-70
type TOPO_DOM
sequence FTKTKSLQTPAN
description Cytoplasmic => ECO:0000269|PubMed:18463093, ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602, ECO:0000269|PubMed:26024518
source Swiss-Prot : SWS_FT_FI3
16) chain A
residue 132-151
type TOPO_DOM
sequence DRYNVIGRPMAASKKMSHRR
description Cytoplasmic => ECO:0000269|PubMed:18463093, ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602, ECO:0000269|PubMed:26024518
source Swiss-Prot : SWS_FT_FI3
17) chain A
residue 225-261
type TOPO_DOM
sequence MSVSNHEKEMAAMAKRLNAKELRKAQAGANAEMRLAK
description Cytoplasmic => ECO:0000269|PubMed:18463093, ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602, ECO:0000269|PubMed:26024518
source Swiss-Prot : SWS_FT_FI3
18) chain A
residue 71-97
type TRANSMEM
sequence MFIINLAFSDFTFSLVNGFPLMTISCF
description Helical; Name=2 => ECO:0000269|PubMed:18463093, ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602, ECO:0000269|PubMed:26024518
source Swiss-Prot : SWS_FT_FI4
19) chain A
residue 305
type MOD_RES
sequence K
description N6-(retinylidene)lysine => ECO:0000269|PubMed:18463093, ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602, ECO:0000269|PubMed:26024518, ECO:0000269|PubMed:3191148, ECO:0007744|PDB:2Z73, ECO:0007744|PDB:4WW3
source Swiss-Prot : SWS_FT_FI10
20) chain A
residue 336
type LIPID
sequence C
description S-palmitoyl cysteine => ECO:0000269|PubMed:18463093, ECO:0007744|PDB:2ZIY
source Swiss-Prot : SWS_FT_FI11
21) chain A
residue 262-283
type TRANSMEM
sequence ISIVIVSQFLLSWSPYAVVALL
description Helical; Name=6 => ECO:0000269|PubMed:18463093, ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602, ECO:0000269|PubMed:26024518
source Swiss-Prot : SWS_FT_FI8
22) chain A
residue 121-137
type prosite
sequence MSIMTMAMISIDRYNVI
description G_PROTEIN_RECEP_F1_1 G-protein coupled receptors family 1 signature. MSImTMAMISIDRYNvI
source prosite : PS00237
23) chain A
residue 299-315
type prosite
sequence LPVMFAKASAIHNPMIY
description OPSIN Visual pigments (opsins) retinal binding site. LPvMfAKASAihNPmiY
source prosite : PS00238
24) chain A
residue 8
type CARBOHYD
sequence N
description N-linked (GlcNAc...) asparagine => ECO:0000305|PubMed:18463093
source Swiss-Prot : SWS_FT_FI13
25) chain A
residue 337
type LIPID
sequence C
description S-palmitoyl cysteine => ECO:0000269|PubMed:18463093, ECO:0000269|PubMed:18480818, ECO:0007744|PDB:2ZIY
source Swiss-Prot : SWS_FT_FI12
26) chain A
residue 110-131
type TRANSMEM
sequence VYGFIGGIFGFMSIMTMAMISI
description Helical; Name=3 => ECO:0000269|PubMed:18463093, ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602, ECO:0000269|PubMed:26024518
source Swiss-Prot : SWS_FT_FI5
27) chain A
residue 152-172
type TRANSMEM
sequence AFIMIIFVWLWSVLWAIGPIF
description Helical; Name=4 => ECO:0000269|PubMed:18463093, ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602, ECO:0000269|PubMed:26024518
source Swiss-Prot : SWS_FT_FI6
28) chain A
residue 200-224
type TRANSMEM
sequence NILCMFILGFFGPILIIFFCYFNIV
description Helical; Name=5 => ECO:0000269|PubMed:18463093, ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602, ECO:0000269|PubMed:26024518
source Swiss-Prot : SWS_FT_FI7
29) chain A
residue 294-315
type TRANSMEM
sequence PYAAQLPVMFAKASAIHNPMIY
description Helical; Name=7 => ECO:0000269|PubMed:18463093, ECO:0000269|PubMed:18480818, ECO:0000269|PubMed:21906602, ECO:0000269|PubMed:26024518
source Swiss-Prot : SWS_FT_FI9

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