3SYS - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   IMPROVED CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA OCCK1 (OPDK)

Authors :   B. Van Den Berg, E. Eren

Date :   18 Jul 11 (Deposition) - 08 Feb 12 (Release) - 08 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Beta-Barrel, Channel, Bacterial Outer Membrane, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Eren, J. Vijayaraghavan, J. Liu, B. R. Cheneke, D. S. Touw, B. W. Lepore, M. Indic, L. Movileanu, B. Van Den Berg
Substrate Specificity Within A Family Of Outer Membrane Carboxylate Channels.
Plos Biol. V. 10 01242 2012
PubMed-ID: 22272184 | Reference-DOI: 10.1371/JOURNAL.PBIO.1001242

Molecule 1 - VANILLATE PORIN OPDK
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 28-417
	Gene	:	OPDK, PA4898
	Organism Scientific	:	PSEUDOMONAS AERUGINOSA
	Organism Taxid	:	287

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 37)

No.	Name	Count	Type	Full Name
1	C8E	29	Ligand/Ion	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
2	EDO	4	Ligand/Ion	1,2-ETHANEDIOL
3	VNL	4	Ligand/Ion	4-HYDROXY-3-METHOXYBENZOATE

Biological Unit 1 (3, 17)

No.	Name	Count	Type	Full Name
1	C8E	14	Ligand/Ion	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	VNL	2	Ligand/Ion	4-HYDROXY-3-METHOXYBENZOATE

Biological Unit 2 (3, 20)

No.	Name	Count	Type	Full Name
1	C8E	15	Ligand/Ion	(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
2	EDO	3	Ligand/Ion	1,2-ETHANEDIOL
3	VNL	2	Ligand/Ion	4-HYDROXY-3-METHOXYBENZOATE

Asymmetric Unit (34, 34)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR A:122 , HOH A:698	BINDING SITE FOR RESIDUE EDO A 399
02	AC2	SOFTWARE	ALA A:211 , LEU A:213 , VAL A:249 , TRP A:316 , C8E A:410 , C8E A:413	BINDING SITE FOR RESIDUE C8E A 400
03	AC3	SOFTWARE	PHE A:253	BINDING SITE FOR RESIDUE C8E A 401
04	AC4	SOFTWARE	LEU A:142 , VAL A:323 , TYR A:325 , C8E A:412	BINDING SITE FOR RESIDUE C8E A 402
05	AC5	SOFTWARE	HIS A:199 , HIS A:260 , TYR A:307 , C8E A:409 , C8E A:411	BINDING SITE FOR RESIDUE C8E A 403
06	AC6	SOFTWARE	GLY A:321 , ARG A:344 , VAL A:346 , C8E A:405	BINDING SITE FOR RESIDUE C8E A 404
07	AC7	SOFTWARE	ASN A:17 , LEU A:364 , HIS A:366 , LEU A:382 , C8E A:404 , HOH A:709	BINDING SITE FOR RESIDUE C8E A 405
08	AC8	SOFTWARE	LEU A:15 , ARG A:16 , ASN A:17 , GLN A:39 , VAL A:384	BINDING SITE FOR RESIDUE C8E A 406
09	AC9	SOFTWARE	LEU A:63 , PHE A:64 , GLY A:93 , VAL A:95 , C8E A:408	BINDING SITE FOR RESIDUE C8E A 407
10	BC1	SOFTWARE	C8E A:407	BINDING SITE FOR RESIDUE C8E A 408
11	BC2	SOFTWARE	C8E A:403	BINDING SITE FOR RESIDUE C8E A 409
12	BC3	SOFTWARE	LEU A:314 , TRP A:316 , C8E A:400	BINDING SITE FOR RESIDUE C8E A 410
13	BC4	SOFTWARE	PHE A:135 , ASN A:180 , TYR A:181 , ALA A:182 , HIS A:199 , ARG A:207 , C8E A:403	BINDING SITE FOR RESIDUE C8E A 411
14	BC5	SOFTWARE	PRO A:143 , TYR A:186 , ARG A:344 , C8E A:402	BINDING SITE FOR RESIDUE C8E A 412
15	BC6	SOFTWARE	LEU A:266 , GLN A:267 , ARG A:301 , SER A:302 , TRP A:303 , HIS A:327 , SER A:329 , C8E A:400	BINDING SITE FOR RESIDUE C8E A 413
16	BC7	SOFTWARE	LYS A:44 , PHE A:45 , ASP A:59 , ALA A:60 , ILE A:61 , GLU A:112 , MET A:113 , LEU A:114 , HOH A:504 , HOH A:548 , HOH A:578	BINDING SITE FOR RESIDUE VNL A 414
17	BC8	SOFTWARE	HIS A:327 , LYS A:340 , TRP A:342 , ARG A:370 , ARG A:371 , SER A:372 , HOH A:695 , HOH A:816	BINDING SITE FOR RESIDUE VNL A 415
18	BC9	SOFTWARE	ALA B:226 , LEU B:252 , SER B:254	BINDING SITE FOR RESIDUE EDO B 399
19	CC1	SOFTWARE	LYS B:268 , GLY B:271 , ASP B:299 , HOH B:530 , HOH B:596	BINDING SITE FOR RESIDUE EDO B 400
20	CC2	SOFTWARE	LEU B:252 , TYR B:263 , ARG B:306 , HOH B:728 , HOH B:790	BINDING SITE FOR RESIDUE EDO B 401
21	CC3	SOFTWARE	GLY B:183	BINDING SITE FOR RESIDUE C8E B 402
22	CC4	SOFTWARE	VAL B:323	BINDING SITE FOR RESIDUE C8E B 403
23	CC5	SOFTWARE	LEU B:43 , GLY B:62 , LEU B:63 , PHE B:64	BINDING SITE FOR RESIDUE C8E B 404
24	CC6	SOFTWARE	ASN B:17 , TYR B:19 , TRP B:37 , HOH B:703	BINDING SITE FOR RESIDUE C8E B 406
25	CC7	SOFTWARE	ASP B:116 , TYR B:122 , ASP B:124 , ARG B:284 , HOH B:781	BINDING SITE FOR RESIDUE C8E B 407
26	CC8	SOFTWARE	VAL B:323 , C8E B:409 , C8E B:410	BINDING SITE FOR RESIDUE C8E B 408
27	CC9	SOFTWARE	PRO B:143 , TYR B:186 , TYR B:325 , TRP B:342 , ARG B:344 , C8E B:408 , C8E B:411	BINDING SITE FOR RESIDUE C8E B 409
28	DC1	SOFTWARE	ALA B:182 , ALA B:184 , HIS B:199 , HIS B:260 , TYR B:307 , VAL B:323 , C8E B:408	BINDING SITE FOR RESIDUE C8E B 410
29	DC2	SOFTWARE	C8E B:409	BINDING SITE FOR RESIDUE C8E B 411
30	DC3	SOFTWARE	TRP A:37 , PHE B:41 , VAL B:66	BINDING SITE FOR RESIDUE C8E B 412
31	DC4	SOFTWARE	ARG B:94 , ASP B:162 , MET B:163	BINDING SITE FOR RESIDUE C8E B 413
32	DC5	SOFTWARE	HIS B:215 , GLY B:225 , PHE B:253 , SER B:254	BINDING SITE FOR RESIDUE C8E B 415
33	DC6	SOFTWARE	LYS B:44 , PHE B:45 , ASP B:59 , ALA B:60 , ILE B:61 , LYS B:109 , GLU B:112 , MET B:113 , LEU B:114 , HOH B:434 , HOH B:533 , HOH B:543 , HOH B:639	BINDING SITE FOR RESIDUE VNL B 417
34	DC7	SOFTWARE	HOH A:552 , HIS B:327 , LYS B:340 , GLU B:341 , TRP B:342 , ARG B:370 , ARG B:371 , SER B:372 , HOH B:561 , HOH B:600 , HOH B:630	BINDING SITE FOR RESIDUE VNL B 418

(no "SS Bond" information available for 3SYS)

Asymmetric Unit

No.	Residues
1	Asn A:76	-	Ser A:77

(no "SAP(SNP)/Variant" information available for 3SYS)

(no "PROSITE Motif" information available for 3SYS)

(no "Exon" information available for 3SYS)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:374
 aligned with Q9HUR5_PSEAE | Q9HUR5 from UniProtKB/TrEMBL  Length:417

    Alignment length:387
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       
         Q9HUR5_PSEAE    31 GFLEDAKTDLVLRNYYFNRDFRDHDAGKSLVDEWAQGFILKFSSGYTPGTVGVGLDAIGLFGVKLNSGRGTSNSELLPLHDDGRAADNYGRVGVAAKLRVSASELKIGEMLPDIPLLRYDDGRLLPQTFRGFAVVSRELPGLALQAGRFDAVSLRNSADMQDLSAWSAPTQKSDGFNYAGAEYRFNRERTQLGLWHGQLEDVYRQSYANLLHKQRVGDWTLGANLGLFVDRDDGAARAGEIDSHTVYGLFSAGIGLHTFYLGLQKVGGDSGWQSVYGSSGRSMGNDMFNGNFTNADERSWQVRYDYDFVGLGWPGLIGMVRYGHGSNATTKAGSGGKEWERDVELGYTVQSGPLARLNVRLNHASNRRSFNSDFDQTRLVVSYPLSW 417
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeeeeee.--------.eeeeeeeeeeeee........eeeeeeeeeeeeee..-----...............eeeeeeeeeeeee..eeeeeeee..ee..ee.........eeeeeeeee.....eeeeeeeeeeee.........eee..eeeeee..eeeeeeeeee....eeeeeeeeee...eeeeeeeeeeeeee..eeeeeeeeeeeeee.........eeeeeeeeeeeee..eeeeeeeeeeee.............................eeeeeeeeee.hhhh...eeeeeeeeeeeee.......eeeeeeeeeeeee.........eeeeeeeeeee.....eeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sys A   4 GFLEDAKTDLVLRNYYFNRDF--------LVDEWAQGFILKFSSGYTPGTVGVGLDAIGLFGVKLNS-----NSELLPLHDDGRAADNYGRVGVAAKLRVSASELKIGEMLPDIPLLRYDDGRLLPQTFRGFAVVSRELPGLALQAGRFDAVSLRNSADMQDLSAWSAPTQKSDGFNYAGAEYRFNRERTQLGLWHGQLEDVYRQSYANLLHKQRVGDWTLGANLGLFVDRDDGAARAGEIDSHTVYGLFSAGIGLHTFYLGLQKVGGDSGWQSVYGSSGRSMGNDMFNGNFTNADERSWQVRYDYDFVGLGWPGLIGMVRYGHGSNATTKAGSGGKEWERDVELGYTVQSGPLARLNVRLNHASNRRSFNSDFDQTRLVVSYPLSW 390
                                    13        23|       33        43        53        63      |  -  |     83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       
                                               24       33                                   70    76

Chain B from PDB  Type:PROTEIN  Length:374
 aligned with Q9HUR5_PSEAE | Q9HUR5 from UniProtKB/TrEMBL  Length:417

    Alignment length:387
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       
         Q9HUR5_PSEAE    31 GFLEDAKTDLVLRNYYFNRDFRDHDAGKSLVDEWAQGFILKFSSGYTPGTVGVGLDAIGLFGVKLNSGRGTSNSELLPLHDDGRAADNYGRVGVAAKLRVSASELKIGEMLPDIPLLRYDDGRLLPQTFRGFAVVSRELPGLALQAGRFDAVSLRNSADMQDLSAWSAPTQKSDGFNYAGAEYRFNRERTQLGLWHGQLEDVYRQSYANLLHKQRVGDWTLGANLGLFVDRDDGAARAGEIDSHTVYGLFSAGIGLHTFYLGLQKVGGDSGWQSVYGSSGRSMGNDMFNGNFTNADERSWQVRYDYDFVGLGWPGLIGMVRYGHGSNATTKAGSGGKEWERDVELGYTVQSGPLARLNVRLNHASNRRSFNSDFDQTRLVVSYPLSW 417
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeeeeeeeeee..------.eeeeeeeeeeeee.......eeeeeeeeeeeeee...-------.............eeeeeeeeeeeee..eeeeeeee..ee..ee.........eeeeeeeee.....eeeeeeeeeeee..........ee..eeeee...eeeeeeeeee....eeeeeeeeee...eeeeeeeeeeeeee..eeeeeeeeeeeeee.........eeeeeeeeeeeee..eeeeeeeeeeee.............................eeeeeeeeee.hhhh...eeeeeeeeeeeeeee..eeeeeeeeeeeeeeee.........eeeeeeeeeee.....eeeeeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sys B   4 GFLEDAKTDLVLRNYYFNRDFRD------LVDEWAQGFILKFSSGYTPGTVGVGLDAIGLFGVKLNS-------ELLPLHDDGRAADNYGRVGVAAKLRVSASELKIGEMLPDIPLLRYDDGRLLPQTFRGFAVVSRELPGLALQAGRFDAVSLRNSADMQDLSAWSAPTQKSDGFNYAGAEYRFNRERTQLGLWHGQLEDVYRQSYANLLHKQRVGDWTLGANLGLFVDRDDGAARAGEIDSHTVYGLFSAGIGLHTFYLGLQKVGGDSGWQSVYGSSGRSMGNDMFNGNFTNADERSWQVRYDYDFVGLGWPGLIGMVRYGHGSNATTKAGSGGKEWERDVELGYTVQSGPLARLNVRLNHASNRRSFNSDFDQTRLVVSYPLSW 390
                                    13        23  |     33        43        53        63      |  -    |   83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       
                                                 26     33                                   70      78

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 3SYS)

(no "CATH Domain" information available for 3SYS)

(no "Pfam Domain" information available for 3SYS)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q9HUR5_PSEAE | Q9HUR5)

molecular function
	GO:0015288	porin activity	Catalysis of the transfer of substances, sized less than 1000 Da, from one side of the membrane to the other. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria.
biological process
	GO:0055085	transmembrane transport	The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.

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	Cis Peptide Bonds
		Asn A:76 - Ser A:77	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 37)

Sites (34, 34)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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