3DP8 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURAL CHARACTERIZATION OF A PUTATIVE ENDOGENOUS METAL CHELATOR IN THE PERIPLASMIC NICKEL TRANSPORTER NIKA (NICKEL BUTANE-1,2,4-TRICARBOXYLATE FORM)

Authors :   M. V. Cherrier, C. Cavazza, C. Bochot, D. Lemaire, J. C. Fontecilla-Cam

Date :   07 Jul 08 (Deposition) - 16 Sep 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)

Keywords :   Nickel, Nickellophore, Butane-1, 2, 4-Tricarboxylate, Transport, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. V. Cherrier, C. Cavazza, C. Bochot, D. Lemaire, J. C. Fontecilla-Camps
Structural Characterization Of A Putative Endogenous Metal Chelator In The Periplasmic Nickel Transporter Nika
Biochemistry V. 47 9937 2008
PubMed-ID: 18759453 | Reference-DOI: 10.1021/BI801051Y

Molecule 1 - NICKEL-BINDING PERIPLASMIC PROTEIN
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET22B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	NIKA, B3476, JW3441
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	K12
	Synonym	:	NIKA

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 33)

No.	Name	Count	Type	Full Name
1	ACT	11	Ligand/Ion	ACETATE ION
2	CL	7	Ligand/Ion	CHLORIDE ION
3	GOL	8	Ligand/Ion	GLYCEROL
4	HCT	3	Ligand/Ion	(2R)-BUTANE-1,2,4-TRICARBOXYLIC ACID
5	NI	3	Ligand/Ion	NICKEL (II) ION
6	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (4, 10)

No.	Name	Count	Type	Full Name
1	ACT	4	Ligand/Ion	ACETATE ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	4	Ligand/Ion	GLYCEROL
4	HCT	1	Ligand/Ion	(2R)-BUTANE-1,2,4-TRICARBOXYLIC ACID
5	NI	-1	Ligand/Ion	NICKEL (II) ION
6	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 9)

No.	Name	Count	Type	Full Name
1	ACT	4	Ligand/Ion	ACETATE ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	4	Ligand/Ion	GLYCEROL
4	HCT	1	Ligand/Ion	(2R)-BUTANE-1,2,4-TRICARBOXYLIC ACID
5	NI	-1	Ligand/Ion	NICKEL (II) ION
6	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 3 (2, 4)

No.	Name	Count	Type	Full Name
1	ACT	3	Ligand/Ion	ACETATE ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	GOL	-1	Ligand/Ion	GLYCEROL
4	HCT	1	Ligand/Ion	(2R)-BUTANE-1,2,4-TRICARBOXYLIC ACID
5	NI	-1	Ligand/Ion	NICKEL (II) ION
6	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (26, 26)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS B:416	BINDING SITE FOR RESIDUE NI B 503
02	AC2	SOFTWARE	HIS C:416	BINDING SITE FOR RESIDUE NI C 503
03	AC3	SOFTWARE	THR C:292 , LEU C:293 , LEU C:455 , HIS C:459 , TYR C:464	BINDING SITE FOR RESIDUE ACT C 504
04	AC4	SOFTWARE	LYS C:330 , ASP C:331 , ILE C:332 , ARG C:365	BINDING SITE FOR RESIDUE ACT C 505
05	AC5	SOFTWARE	SER A:57 , GLU A:58	BINDING SITE FOR RESIDUE ACT A 505
06	AC6	SOFTWARE	GLU B:221 , LEU B:226 , PHE B:229 , LEU B:283 , THR B:286 , MET B:473	BINDING SITE FOR RESIDUE ACT B 504
07	AC7	SOFTWARE	GLN C:385 , HIS C:395 , ARG C:396 , TRP C:398 , HIS C:416	BINDING SITE FOR RESIDUE ACT C 506
08	AC8	SOFTWARE	GLN A:288 , THR B:286 , GLN B:288	BINDING SITE FOR RESIDUE ACT A 506
09	AC9	SOFTWARE	ARG B:341 , LYS C:433	BINDING SITE FOR RESIDUE ACT B 505
10	BC1	SOFTWARE	TYR B:271 , LYS B:306 , PRO B:307 , HIS B:459	BINDING SITE FOR RESIDUE ACT B 506
11	BC2	SOFTWARE	THR B:8 , ALA B:9 , LEU B:216 , LEU B:217 , TYR B:218 , LEU B:223	BINDING SITE FOR RESIDUE ACT B 507
12	BC3	SOFTWARE	ASP A:93 , ASN A:94 , ARG A:95 , GLN A:96 , GLN C:446	BINDING SITE FOR RESIDUE ACT A 507
13	BC4	SOFTWARE	GLN A:361 , SER A:372 , LEU A:373	BINDING SITE FOR RESIDUE SO4 A 508
14	BC5	SOFTWARE	THR B:441 , HIS B:442	BINDING SITE FOR RESIDUE CL B 508
15	BC6	SOFTWARE	LEU B:293 , HIS B:459	BINDING SITE FOR RESIDUE CL B 509
16	BC7	SOFTWARE	TYR B:22 , ARG B:97 , ARG B:137 , TRP B:398 , HIS B:416	BINDING SITE FOR RESIDUE HCT B 511
17	BC8	SOFTWARE	TYR A:22 , ARG A:97 , TRP A:100 , ARG A:137 , TRP A:398 , HIS A:416	BINDING SITE FOR RESIDUE HCT A 511
18	BC9	SOFTWARE	TYR C:22 , MET C:27 , ARG C:97 , TRP C:100 , ARG C:137 , ARG C:396 , TRP C:398 , HIS C:416	BINDING SITE FOR RESIDUE HCT C 509
19	CC1	SOFTWARE	ASN A:274 , LYS A:276 , ASP A:280 , LYS A:316 , GLU A:320 , LEU A:326 , ARG A:333	BINDING SITE FOR RESIDUE GOL A 512
20	CC2	SOFTWARE	PRO B:48 , LYS B:52 , SER B:53 , TRP B:54	BINDING SITE FOR RESIDUE GOL B 512
21	CC3	SOFTWARE	THR A:349 , GLU A:376 , GLU A:377 , GLU A:378	BINDING SITE FOR RESIDUE GOL A 513
22	CC4	SOFTWARE	ASN B:254 , ALA B:256 , LYS B:257 , ASP B:387 , GLY B:388 , GLN B:420 , GLN B:423	BINDING SITE FOR RESIDUE GOL B 513
23	CC5	SOFTWARE	SER B:57 , GLU B:58	BINDING SITE FOR RESIDUE GOL B 514
24	CC6	SOFTWARE	ALA A:42 , ASP A:43 , GLN B:41 , ALA B:42 , TYR B:485 , PRO B:487	BINDING SITE FOR RESIDUE GOL A 514
25	CC7	SOFTWARE	LYS B:354 , GLU B:358	BINDING SITE FOR RESIDUE GOL A 515
26	CC8	SOFTWARE	ARG A:389 , GLU B:358 , GLN B:361 , SER B:372 , LEU B:373	BINDING SITE FOR RESIDUE GOL B 515

(no "SS Bond" information available for 3DP8)

Asymmetric Unit

No.	Residues
1	Pro A:3	-	Asp A:4
2	Thr A:23	-	Pro A:24
3	Arg A:137	-	Pro A:138
4	Ala A:258	-	Pro A:259
5	Ala A:400	-	Pro A:401
6	Asp A:403	-	Pro A:404
7	Thr B:23	-	Pro B:24
8	Arg B:137	-	Pro B:138
9	Ala B:258	-	Pro B:259
10	Tyr B:284	-	Gly B:285
11	Gly B:285	-	Thr B:286
12	Ala B:400	-	Pro B:401
13	Asp B:403	-	Pro B:404
14	Thr C:23	-	Pro C:24
15	Arg C:137	-	Pro C:138
16	Ala C:258	-	Pro C:259
17	Ala C:400	-	Pro C:401
18	Asp C:403	-	Pro C:404

(no "SAP(SNP)/Variant" information available for 3DP8)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SBP_BACTERIAL_5	PS01040	Bacterial extracellular solute-binding proteins, family 5 signature.	NIKA_ECOLI	73-95	3	A:51-73 B:51-73 C:51-73

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SBP_BACTERIAL_5	PS01040	Bacterial extracellular solute-binding proteins, family 5 signature.	NIKA_ECOLI	73-95	1	A:51-73 - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SBP_BACTERIAL_5	PS01040	Bacterial extracellular solute-binding proteins, family 5 signature.	NIKA_ECOLI	73-95	1	- B:51-73 -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SBP_BACTERIAL_5	PS01040	Bacterial extracellular solute-binding proteins, family 5 signature.	NIKA_ECOLI	73-95	1	- - C:51-73

(no "Exon" information available for 3DP8)

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:498
 aligned with NIKA_ECOLI | P33590 from UniProtKB/Swiss-Prot  Length:524

    Alignment length:498
                                    33        43        53        63        73        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       393       403       413       423       433       443       453       463       473       483       493       503       513        
           NIKA_ECOLI    24 APDEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQITLKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELGNIPYAPIATEIPFEQIKP 521
               SCOP domains d3dp8a_ A: Nickel-binding periplasmic protein NikA                                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee...............hhhhhhhhh...eee.....eee..eeeeee.....eeeeee............hhhhhhhhhhhhhhhhhhhh.hhhhhheeeeee....eeeeee.....hhhhhhh........hhhhh.................eeeeeee...eeeeee............eeeeee..hhhhhhhhhhh....eeee.....hhhhhhhhhh....eeeeeeeeeeeeeee........hhhhhhhhhhhhhhhhhhhhhh....ee.....................hhhhhhhhhhhh...........ee..ee.eeeeeee..hhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhh...eeeee.......hhhhhhhh....hhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeee.hhhh...........hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------SBP_BACTERIAL_5        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3dp8 A   2 APDEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQITLKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELGNIPYAPIATEIPFEQIKP 499
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491

Chain B from PDB  Type:PROTEIN  Length:497
 aligned with NIKA_ECOLI | P33590 from UniProtKB/Swiss-Prot  Length:524

    Alignment length:498
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514        
           NIKA_ECOLI    25 PDEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQITLKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELGNIPYAPIATEIPFEQIKPV 522
               SCOP domains d3dp8b_ B: Nickel-binding periplasmic protein NikA                                                                                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee...............hhhhhhhhh...eee.....eee..eeeeee.....eeeeee............hhhhhhhhhhhhhhhhhhhh.hhhhhheeeeee....eeeeee.....hhhhhhh........hhhhh.................eeeeeee...eeeeee............eeeeee..hhhhhhhhhhh....eeeee....hhhhhhhhhh....eeee....eeeeeee........hhhhhhhhhhhhhhhhhhhh..........................-..hhhhhhhhhhhh...........ee..ee.eeeeeee..hhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhh...eeeee.......hhhhhhhhhh...hhhhhh....hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..eeeeeee.eeeee.hhhh...........hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------SBP_BACTERIAL_5        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3dp8 B   3 PDEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQITLKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKP-QYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELGNIPYAPIATEIPFEQIKPV 500
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302    | |312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492        
                                                                                                                                                                                                                                                                                                                                          307 |                                                                                                                                                                                               
                                                                                                                                                                                                                                                                                                                                            309

Chain C from PDB  Type:PROTEIN  Length:496
 aligned with NIKA_ECOLI | P33590 from UniProtKB/Swiss-Prot  Length:524

    Alignment length:496
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515      
           NIKA_ECOLI    26 DEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQITLKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELGNIPYAPIATEIPFEQIKP 521
               SCOP domains d3dp8c_ C: Nickel-binding periplasmic protein NikA                                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...............hhhhhhhhh...eee.....eee....eeee.....eeeee.............hhhhhhhhhhhhhhhhhhhh.hhhhhheeeeee....eeeeee.....hhhhhhh........hhhhh.................eeeeeee...eeeeee............eeeeee..hhhhhhhhhhh....eeeee....hhhhhhhhhh....eeee....eeeeeee........hhhhhhhhhhhhhhhhhhhh......ee.....................hhhhhhhhhhhh...........ee..ee.eeeeeee..hhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhh...eeeee.......hhhhhhhh.....hhhhhh....hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh..eeeeeee.eeeee.hhhh...........hhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------SBP_BACTERIAL_5        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dp8 C   4 DEITTAWPVNVGPLNPHLYTPNQMFAQSMVYEPLVKYQADGSVIPWLAKSWTHSEDGKTWTFTLRDDVKFSNGEPFDAEAAAENFRAVLDNRQRHAWLELANQIVDVKALSKTELQITLKSAYYPFLQELALPRPFRFIAPSQFKNHETMNGIKAPIGTGPWILQESKLNQYDVFVRNENYWGEKPAIKKITFNVIPDPTTRAVAFETGDIDLLYGNEGLLPLDTFARFSQNPAYHTQLSQPIETVMLALNTAKAPTNELAVREALNYAVNKKSLIDNALYGTQQVADTLFAPSVPYANLGLKPSQYDPQKAKALLEKAGWTLPAGKDIREKNGQPLRIELSFIGTDALSKSMAEIIQADMRQIGADVSLIGEEESSIYARQRDGRFGMIFHRTWGAPYDPHAFLSSMRVPSHADFQAQQGLADKPLIDKEIGEVLATHDETQRQALYRDILTRLHDEAVYLPISYISMMVVSKPELGNIPYAPIATEIPFEQIKP 499
                                    13        23        33        43        53        63        73        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       393       403       413       423       433       443       453       463       473       483       493

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Periplasmic binding protein-like II (813)

Superfamily: Periplasmic binding protein-like II (813)

Family: Phosphate binding protein-like (463)

Protein domain: Nickel-binding periplasmic protein NikA (18)

Escherichia coli [TaxId: 562] (18)

1a	d3dp8a_	A:
1b	d3dp8b_	B:
1c	d3dp8c_	C:

(no "CATH Domain" information available for 3DP8)

(no "Pfam Domain" information available for 3DP8)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (NIKA_ECOLI | P33590)

molecular function
	GO:0020037	heme binding	Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
	GO:0016151	nickel cation binding	Interacting selectively and non-covalently with nickel (Ni) cations.
	GO:0015197	peptide transporter activity	Enables the directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells.
	GO:0046914	transition metal ion binding	Interacting selectively and non-covalently with a transition metal ions; a transition metal is an element whose atom has an incomplete d-subshell of extranuclear electrons, or which gives rise to a cation or cations with an incomplete d-subshell. Transition metals often have more than one valency state. Biologically relevant transition metals include vanadium, manganese, iron, copper, cobalt, nickel, molybdenum and silver.
biological process
	GO:0050919	negative chemotaxis	The directed movement of a motile cell or organism towards a lower concentration of a chemical.
	GO:0015675	nickel cation transport	The directed movement of nickel (Ni) cations into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0015833	peptide transport	The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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:0043190	ATP-binding cassette (ABC) transporter complex	A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
	GO:0030288	outer membrane-bounded periplasmic space	The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
	GO:0042597	periplasmic space	The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

Asymmetric Unit
	Complete Structure
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Ala A:258 - Pro A:259	[ RasMol ]
		Ala A:400 - Pro A:401	[ RasMol ]
		Ala B:258 - Pro B:259	[ RasMol ]
		Ala B:400 - Pro B:401	[ RasMol ]
		Ala C:258 - Pro C:259	[ RasMol ]
		Ala C:400 - Pro C:401	[ RasMol ]
		Arg A:137 - Pro A:138	[ RasMol ]
		Arg B:137 - Pro B:138	[ RasMol ]
		Arg C:137 - Pro C:138	[ RasMol ]
		Asp A:403 - Pro A:404	[ RasMol ]
		Asp B:403 - Pro B:404	[ RasMol ]
		Asp C:403 - Pro C:404	[ RasMol ]
		Gly B:285 - Thr B:286	[ RasMol ]
		Pro A:3 - Asp A:4	[ RasMol ]
		Thr A:23 - Pro A:24	[ RasMol ]
		Thr B:23 - Pro B:24	[ RasMol ]
		Thr C:23 - Pro C:24	[ RasMol ]
		Tyr B:284 - Gly B:285	[ RasMol ]

Biological Units
	Complete Structure
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		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

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Access by PDB/NDB ID
	3dp8
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1uiu	NIKA - NICKEL UNLIGANDED FORM
1uiv	NIKA - NICKEL LIGANDED FORM
1zlq	NIKA - FEEDTA
2noo	NIKA MUTANT

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 33)

Sites (26, 26)

SS Bonds (0, 0)

Cis Peptide Bonds (18, 18)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 3)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 3)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (12, 12)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File