1CWQ

M INTERMEDIATE STRUCTURE OF THE WILD TYPE BACTERIORHODOPSIN IN COMBINATION WITH THE GROUND STATE STRUCTURE

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005216	molecular_function	monoatomic ion channel activity
A	0005886	cellular_component	plasma membrane
A	0006811	biological_process	monoatomic ion transport
A	0007602	biological_process	phototransduction
A	0009881	molecular_function	photoreceptor activity
A	0015454	molecular_function	light-driven active monoatomic ion transmembrane transporter activity
A	0016020	cellular_component	membrane
A	1902600	biological_process	proton transmembrane transport
B	0005216	molecular_function	monoatomic ion channel activity
B	0005886	cellular_component	plasma membrane
B	0006811	biological_process	monoatomic ion transport
B	0007602	biological_process	phototransduction
B	0009881	molecular_function	photoreceptor activity
B	0015454	molecular_function	light-driven active monoatomic ion transmembrane transporter activity
B	0016020	cellular_component	membrane
B	1902600	biological_process	proton transmembrane transport

Functional Information from PDB Data

site_id	AC1
Number of Residues	25
Details	BINDING SITE FOR RESIDUE RET A 601

Chain	Residue
A	TRP86
A	PRO186
A	TRP189
A	ASP212
A	LYS216
B	TYR83
B	TRP86
B	THR89
B	SER141
B	THR142
B	TRP182
A	THR90
B	TYR185
B	PRO186
B	ASP212
B	ALA215
B	LYS216
B	RET601
A	LEU93
A	MET118
A	TRP138
A	SER141
A	THR142
A	TRP182
A	TYR185

---

site_id	AC2
Number of Residues	26
Details	BINDING SITE FOR RESIDUE RET B 601

Chain	Residue
A	TRP86
A	THR89
A	THR90
A	LEU93
A	MET118
A	TRP138
A	SER141
A	THR142
A	TRP182
A	PRO186
A	TRP189
A	LYS216
A	RET601
B	TYR83
B	TRP86
B	THR89
B	MET118
B	ILE119
B	TRP138
B	SER141
B	THR142
B	TRP182
B	TYR185
B	PRO186
B	ALA215
B	LYS216

---

site_id	AC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE UND A 604

Chain	Residue
A	LEU146
A	TYR147
A	PHE154
A	VAL173
A	ILE222
A	UND1604
B	LEU146
B	TYR147
B	TYR150
B	PHE154

---

site_id	AC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE OCT A 605

Chain	Residue
A	PHE135
A	ALA139
A	HEX606
A	OCT623
A	OCT1605
A	HEX1606
B	PHE135
B	VAL136
B	ALA139

---

site_id	AC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE HEX A 606

Chain	Residue
A	LEU15
A	VAL210
A	OCT605
A	UND624
A	HEX1606
A	UND1624

---

site_id	AC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE OCT B 607

Chain	Residue
A	ILE52
A	PHE88
A	GLY116
B	ILE52
B	PHE88
B	GLY113
B	ILE117
B	OCT1607

---

site_id	AC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE HEX A 608

Chain	Residue
A	VAL217
A	HEX1608
B	VAL217
B	UND1614

---

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE OCT B 609

Chain	Residue
B	ARG175
B	ASN176
B	OCT1609
B	OCT1609

---

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE HEX A 610

Chain	Residue
A	LEU87
A	VAL112
A	HEX1610
B	VAL112

---

site_id	BC1
Number of Residues	17
Details	BINDING SITE FOR RESIDUE TRD B 611

Chain	Residue
A	PHE54
A	ALA110
A	TYR147
A	HOH871
B	GLY21
B	THR24
B	ALA44
B	LEU48
B	PHE54
B	ALA110
B	ILE140
B	ALA144
B	TYR147
B	TRD1611
A	GLY21
A	THR47
A	LEU48

---

site_id	BC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE TRD A 612

Chain	Residue
A	LEU28
A	OCT623
A	TRD1612

---

site_id	BC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE OCT B 613

Chain	Residue
A	LEU22
B	LEU22
B	UND614
B	OCT1613
B	OCT1613

---

site_id	BC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE UND B 614

Chain	Residue
A	LEU25
A	VAL29
B	LEU25
B	VAL29
B	OCT613
B	OCT1613
B	UND1614

---

site_id	BC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE TRD B 615

Chain	Residue
A	LYS41
A	LEU95
A	LEU99
A	HEX1610
A	TRD1615
B	PRO91
B	GLN105

---

site_id	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE UND B 616

Chain	Residue
A	ILE198
B	ILE198
B	ILE198
B	UND1616
B	UND1616

---

site_id	BC7
Number of Residues	2
Details	BINDING SITE FOR RESIDUE OCT A 617

Chain	Residue
A	UND1604
A	OCT1617

---

site_id	BC8
Number of Residues	9
Details	BINDING SITE FOR RESIDUE OCT B 618

Chain	Residue
A	TRP138
A	LEU190
A	HEX620
A	OCT1617
B	TRP138
B	LEU190
B	UND1616
B	OCT1618
B	HEX1620

---

site_id	BC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE HEX B 619

Chain	Residue
A	TYR26
A	VAL29
B	VAL29
B	HEX1619

---

site_id	CC1
Number of Residues	9
Details	BINDING SITE FOR RESIDUE HEX A 620

Chain	Residue
A	LEU146
A	SER183
A	VAL187
A	OCT1617
B	MET145
B	SER183
B	VAL187
B	OCT618
B	HEX1620

---

site_id	CC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE OCT B 621

Chain	Residue
A	OCT1621
A	OCT1621

---

site_id	CC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE HEX B 622

Chain	Residue
A	TRP80
A	HEX1622
B	TRP80
B	HOH821

---

site_id	CC4
Number of Residues	12
Details	BINDING SITE FOR RESIDUE OCT A 623

Chain	Residue
A	PHE135
A	TRP138
A	LEU206
A	OCT605
A	TRD612
A	OCT1605
A	OCT1623
B	PHE135
B	TRP138
B	ILE203
B	HOH803
B	HOH1803

---

site_id	CC5
Number of Residues	3
Details	BINDING SITE FOR RESIDUE UND A 624

Chain	Residue
A	HEX606
A	HEX1606
A	UND1624

---

site_id	CC6
Number of Residues	11
Details	BINDING SITE FOR RESIDUE UND A 1604

Chain	Residue
A	VAL173
A	VAL177
A	ILE222
A	UND604
A	OCT617
A	TRD1612
A	OCT1617
B	LEU146
B	TYR147
B	VAL173
B	ILE222

---

site_id	CC7
Number of Residues	9
Details	BINDING SITE FOR RESIDUE OCT A 1605

Chain	Residue
A	TRP12
A	SER132
A	LEU206
A	OCT605
A	OCT623
A	HOH854
B	TRP12
B	SER132
B	PHE135

---

site_id	CC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE HEX A 1606

Chain	Residue
A	TRP12
A	LEU15
A	OCT605
A	HEX606
A	UND624
B	TRP12

---

site_id	CC9
Number of Residues	10
Details	BINDING SITE FOR RESIDUE OCT B 1607

Chain	Residue
A	ILE52
A	GLY113
A	GLY116
A	ILE117
B	ILE52
B	PHE88
B	GLY113
B	GLY116
B	ILE117
B	OCT607

---

site_id	DC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE HEX A 1608

Chain	Residue
A	LEU19
A	GLY23
A	HEX608
B	LEU19
B	GLY23
B	TYR26

---

site_id	DC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE OCT B 1609

Chain	Residue
B	OCT609
B	OCT609

---

site_id	DC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE HEX A 1610

Chain	Residue
A	LEU87
A	VAL112
A	HEX610
A	TRD1615
B	VAL112
B	TRD615

---

site_id	DC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE TRD B 1611

Chain	Residue
A	THR47
A	TYR147
A	HOH871
A	HOH1872
B	LEU48
B	PHE54
B	TYR147
B	TRD611

---

site_id	DC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE TRD A 1612

Chain	Residue
A	LEU28
A	MET32
A	LEU146
A	TRD612
A	UND1604
B	LEU146

---

site_id	DC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE OCT B 1613

Chain	Residue
A	LEU22
B	LEU22
B	OCT613
B	OCT613
B	UND614

---

site_id	DC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE UND B 1614

Chain	Residue
A	LEU19
A	HEX608
B	LEU19
B	LEU25
B	VAL29
B	UND614

---

site_id	DC8
Number of Residues	9
Details	BINDING SITE FOR RESIDUE TRD A 1615

Chain	Residue
A	LEU99
A	GLN105
A	ILE108
A	HEX1610
B	PRO91
B	LEU92
B	GLN105
B	ILE108
B	TRD615

---

site_id	DC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE UND B 1616

Chain	Residue
B	ILE198
B	UND616
B	UND616
B	OCT618

---

site_id	EC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE OCT A 1617

Chain	Residue
A	ASN176
A	OCT617
A	HEX620
A	UND1604
B	OCT618

---

site_id	EC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE OCT B 1618

Chain	Residue
A	OCT1623
B	TRP138
B	LEU190
B	OCT618

---

site_id	EC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE HEX B 1619

Chain	Residue
A	TYR26
B	TYR26
B	VAL29
B	HEX619

---

site_id	EC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE HEX B 1620

Chain	Residue
A	THR142
A	SER183
A	HEX620
B	THR142
B	MET145
B	SER183
B	OCT618

---

site_id	EC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE OCT A 1621

Chain	Residue
B	OCT621
B	OCT621

---

site_id	EC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE HEX A 1622

Chain	Residue
A	LEU123
B	LEU123
B	HEX622

---

site_id	EC7
Number of Residues	10
Details	BINDING SITE FOR RESIDUE OCT A 1623

Chain	Residue
A	ILE203
A	LEU207
A	OCT623
B	PHE135
B	ILE203
B	LEU206
B	LEU207
B	HOH803
B	OCT1618
B	HOH1803

---

site_id	EC8
Number of Residues	3
Details	BINDING SITE FOR RESIDUE UND A 1624

Chain	Residue
A	VAL136
A	HEX606
A	UND624

---

Functional Information from PROSITE/UniProt

site_id	PS00327
Number of Residues	12
Details	BACTERIAL_OPSIN_RET Bacterial rhodopsins retinal binding site. FMVLDVsAKvGF

Chain	Residue	Details
A	PHE208-PHE219

---

site_id	PS00950
Number of Residues	13
Details	BACTERIAL_OPSIN_1 Bacterial rhodopsins signature 1. RYaDWlFTTPLLL

Chain	Residue	Details
A	ARG82-LEU94

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	38
Details	Transmembrane: {"description":"Helical; Name=Helix A","evidences":[{"source":"PubMed","id":"10452895","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"28008064","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1C3W","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	80
Details	Topological domain: {"description":"Cytoplasmic","evidences":[{"source":"PubMed","id":"10452895","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"28008064","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1C3W","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	36
Details	Transmembrane: {"description":"Helical; Name=Helix B","evidences":[{"source":"PubMed","id":"10452895","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"28008064","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1C3W","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	66
Details	Topological domain: {"description":"Extracellular","evidences":[{"source":"PubMed","id":"10452895","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"28008064","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1C3W","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	32
Details	Transmembrane: {"description":"Helical; Name=Helix C","evidences":[{"source":"PubMed","id":"10452895","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"28008064","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1C3W","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	38
Details	Transmembrane: {"description":"Helical; Name=Helix D","evidences":[{"source":"PubMed","id":"10452895","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"28008064","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1C3W","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	38
Details	Transmembrane: {"description":"Helical; Name=Helix E","evidences":[{"source":"PubMed","id":"10452895","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"28008064","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1C3W","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	36
Details	Transmembrane: {"description":"Helical; Name=Helix F","evidences":[{"source":"PubMed","id":"10452895","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"28008064","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1C3W","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	38
Details	Transmembrane: {"description":"Helical; Name=Helix G","evidences":[{"source":"PubMed","id":"10452895","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"28008064","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1C3W","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	2
Details	Site: {"description":"Primary proton acceptor","evidences":[{"source":"PubMed","id":"10903866","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"10949309","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"28008064","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	2
Details	Modified residue: {"description":"N6-(retinylidene)lysine","evidences":[{"source":"PubMed","id":"10452895","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"10467143","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"10548112","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"10903866","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"10949307","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"10949309","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"11829498","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"28008064","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"6794028","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9287223","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9632391","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9751724","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1C3W","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1F50","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1IW9","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1KG8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1KG9","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1M0L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1M0M","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1O0A","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1P8H","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1P8U","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1Q5J","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1QHJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1QKP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1QM8","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1R2N","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1R84","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1S8J","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TN0","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1TN5","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1UCQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1X0I","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1X0K","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1X0S","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1XJI","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2AT9","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2BRD","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2I1X","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2I20","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2I21","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2NTU","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2NTW","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2WJK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2WJL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZFE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2ZZL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3COD","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3HAN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3HAO","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3HAP","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3HAQ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3HAR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3HAS","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3NS0","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3NSB","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3T45","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3UTV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3UTW","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3UTX","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3VHZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3VI0","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4FPD","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4HWL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4MD1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4MD2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4X31","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4X32","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5A44","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5A45","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5B34","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5B6V","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5B6W","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5B6X","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5B6Y","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5B6Z","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5BR2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5BR5","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5H2H","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5H2I","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5H2J","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5H2K","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5H2L","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5H2M","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5H2N","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5H2O","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5H2P","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"5J7A","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---