1NIP - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTALLOGRAPHIC STRUCTURE OF THE NITROGENASE IRON PROTEIN FROM AZOTOBACTER VINELANDII

Authors :   H. Komiya, M. M. Georgiadis, P. Chakrabarti, D. Woo, J. J. Kornuc, D. C. Rees

Date :   29 Sep 92 (Deposition) - 31 Oct 93 (Release) - 24 Mar 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

Chains :   Asym./Biol. Unit : A,B

Keywords :   Iron Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. M. Georgiadis, H. Komiya, P. Chakrabarti, D. Woo, J. J. Kornuc, D. C. Rees
Crystallographic Structure Of The Nitrogenase Iron Protein From Azotobacter Vinelandii.
Science V. 257 1653 1992
PubMed-ID: 1529353
(for further references see the PDB file header)

Molecule 1 - NITROGENASE IRON PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Organism Scientific	:	AZOTOBACTER VINELANDII
	Organism Taxid	:	354

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 4)

No.	Name	Count	Type	Full Name
1	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	SF4	1	Ligand/Ion	IRON/SULFUR CLUSTER

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:14 , SER A:16 , HOH A:5011 , HOH A:5013 , ADP B:292 , HOH B:5012 , HOH B:5014	BINDING SITE FOR RESIDUE MG A 291
2	AC2	SOFTWARE	GLY B:14 , SER B:16 , HOH B:5025 , HOH B:5026 , HOH B:5027 , HOH B:5028	BINDING SITE FOR RESIDUE MG B 291
3	AC3	SOFTWARE	CYS A:97 , ALA A:98 , CYS A:132 , GLY A:133 , GLY A:134 , CYS B:97 , ALA B:98 , CYS B:132 , GLY B:134 , PHE B:135	BINDING SITE FOR RESIDUE SF4 B 290
4	AC4	SOFTWARE	GLY A:11 , GLY A:12 , ILE A:13 , LYS A:41 , ALA A:42 , MG A:291 , HOH A:5013 , LYS B:10 , GLY B:11 , GLY B:128 , ASP B:129 , MET B:156 , ALA B:160 , HOH B:298 , HOH B:5012 , HOH B:5014	BINDING SITE FOR RESIDUE ADP B 292
5	ATP	AUTHOR	ASP A:39 , ASP A:43 , ASP B:39 , ASP B:43	A POSSIBLE SITE FOR ATP HYDROLYSIS
6	FES	AUTHOR	CYS A:97 , CYS A:132 , CYS B:97 , CYS B:132	THE 4S-FE CLUSTER
7	WMA	AUTHOR	GLY A:9 , LYS A:10 , GLY A:11 , GLY A:12 , ILE A:13 , GLY A:14 , LYS A:15 , SER A:16 , GLY B:9 , LYS B:10 , GLY B:11 , GLY B:12 , ILE B:13 , GLY B:14 , LYS B:15 , SER B:16	WALKER A MOTIF
8	WMB	AUTHOR	ASP A:125 , ASP B:125	WALKER B MOTIF

(no "SS Bond" information available for 1NIP)

(no "Cis Peptide Bond" information available for 1NIP)

(no "SAP(SNP)/Variant" information available for 1NIP)

Asymmetric/Biological Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NIFH_FRXC_3	PS51026	NIFH_FRXC family profile.	NIFH1_AZOVI	3-275	2	A:2-274 B:2-274
2	NIFH_FRXC_1	PS00746	NifH/frxC family signature 1.	NIFH1_AZOVI	88-100	2	A:87-99 B:87-99
3	NIFH_FRXC_2	PS00692	NifH/frxC family signature 2.	NIFH1_AZOVI	126-139	2	A:125-138 B:125-138

(no "Exon" information available for 1NIP)

Asymmetric/Biological 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:283
 aligned with NIFH1_AZOVI | P00459 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:283
                                    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   
          NIFH1_AZOVI     2 AMRQCAIYGKGGIGKSTTTQNLVAALAEMGKKVMIVGCDPKADSTRLILHSKAQNTIMEMAAEAGTVEDLELEDVLKAGYGGVKCVESGGPEPGVGCAGRGVITAINFLEEEGAYEDDLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANNISKGIVKYANSGSVRLGGLICNSRNTDREDELIIALANKLGTQMIHFVPRDNVVQRAEIRRMTVIEYDPKAKQADEYRALARKVVDNKLLVIPNPITMDELEELLMEFGIMEVEDESIVG 284
               SCOP domains d1nipa_ A: Nitrogenase iron protein                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1nipA00 A:1-283 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.....hhhhhhhhhhhhhhhh...eeeee..................hhhhhhhhhh.....hhhhhheeehhheeeee.........hhhhhhhhhhhhhhhh........eeeee.hhhhhhhhhhhhhhh....eeeeee......hhhhhhhhhhhhhh......eeeeeeee.....hhhhhhhhhhhhhh....eee...hhhhhhhh...........hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -NIFH_FRXC_3  PDB: A:2-274 UniProt: 3-275                                                                                                                                                                                                                                         --------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------NIFH_FRXC_1  -------------------------NIFH_FRXC_2   ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nip A   1 AMRQCAIYGKGGIGKSTTTQNLVAALAEMGKKVMIVGCDPKADSTRLILHSKAQNTIMEMAAEAGTVEDLELEDVLKAGYGGVKCVESGGPEPGVGCAGRGVITAINFLEEEGAYEDDLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANNISKGIVKYANSGSVRLGGLICNSRNTDREDELIIALANKLGTQMIHFVPRDNVVQRAEIRRMTVIEYDPKAKQADEYRALARKVVDNKLLVIPNPITMDELEELLMEFGIMEVEDESIVG 283
                                    10        20        30        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

Chain B from PDB  Type:PROTEIN  Length:287
 aligned with NIFH1_AZOVI | P00459 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:287
                                    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       
          NIFH1_AZOVI     2 AMRQCAIYGKGGIGKSTTTQNLVAALAEMGKKVMIVGCDPKADSTRLILHSKAQNTIMEMAAEAGTVEDLELEDVLKAGYGGVKCVESGGPEPGVGCAGRGVITAINFLEEEGAYEDDLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANNISKGIVKYANSGSVRLGGLICNSRNTDREDELIIALANKLGTQMIHFVPRDNVVQRAEIRRMTVIEYDPKAKQADEYRALARKVVDNKLLVIPNPITMDELEELLMEFGIMEVEDESIVGKTAE 288
               SCOP domains d1nipb_ B: Nitrogenase iron protein                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1nipB00 B:1-287 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                                                                            CATH domains
           Pfam domains (1) --Fer4_NifH-1nipB01 B:3-275                                                                                                                                                                                                                                                        ------------ Pfam domains (1)
           Pfam domains (2) --Fer4_NifH-1nipB02 B:3-275                                                                                                                                                                                                                                                        ------------ Pfam domains (2)
         Sec.struct. author ..eeeee......hhhhhhhhhhhhhhhhh..eeeee..................hhhhhhhhhh.....hhhhhh..hhhhheeee.........hhhhhhhhhhhhhhhh........eeeee......hhhhhhhhhh....eee.....hhhhhhhhhhhhhhhhhhhh....ee.eeeee.....hhhhhhhhhhhhhh.eeeeee...hhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -NIFH_FRXC_3  PDB: B:2-274 UniProt: 3-275                                                                                                                                                                                                                                         ------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------NIFH_FRXC_1  -------------------------NIFH_FRXC_2   ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nip B   1 AMRQCAIYGKGGIGKSTTTQNLVAALAEMGKKVMIVGCDPKADSTRLILHSKAQNTIMEMAAEAGTVEDLELEDVLKAGYGGVKCVESGGPEPGVGCAGRGVITAINFLEEEGAYEDDLDFVFYDVLGDVVCGGFAMPIRENKAQEIYIVCSGEMMAMYAANNISKGIVKYANSGSVRLGGLICNSRNTDREDELIIALANKLGTQMIHFVPRDNVVQRAEIRRMTVIEYDPKAKQADEYRALARKVVDNKLLVIPNPITMDELEELLMEFGIMEVEDESIVGKTAE 287
                                    10        20        30        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

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: Nitrogenase iron protein-like (152)

Protein domain: Nitrogenase iron protein (21)

Azotobacter vinelandii [TaxId: 354] (20)

1a	d1nipa_	A:
1b	d1nipb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Azotobacter vinelandii. Organism_taxid: 354 (3)

1a	1nipA00	A:1-283
1b	1nipB00	B:1-287

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: Fer4_NifH (10)

Azotobacter vinelandii (10)

1a	Fer4_NifH-1nipB01	B:3-275
1b	Fer4_NifH-1nipB02	B:3-275

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (NIFH1_AZOVI | P00459)

molecular function
	GO:0051539	4 iron, 4 sulfur cluster binding	Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0018697	carbonyl sulfide nitrogenase activity	Catalysis of the reaction: carbonyl sulfide + 2 H+ + 2 e- = hydrogen sulfide + carbon monoxide.
	GO:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016163	nitrogenase activity	Catalysis of the reaction: 8 reduced ferredoxin + 8 H+ + nitrogen + 16 ATP = 8 oxidized ferredoxin + 2 NH3 + 16 ADP + 16 phosphate.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0009399	nitrogen fixation	The process in which nitrogen is taken from its relatively inert molecular form (N2) in the atmosphere and converted into nitrogen compounds useful for other chemical processes, such as ammonia, nitrate and nitrogen dioxide.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0016612	molybdenum-iron nitrogenase complex	An enzyme complex containing a molybdenum-iron cluster found in many species. It is composed of two proteins, dinitrogenase and nitrogenase reductase; dinitrogenase, the molybdenum-iron protein, is tetrameric with an alpha2-beta2 structure, and nitrogenase reductase is a homodimer.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		ADP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SF4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		ATP	[ RasMol ]	+environment [ RasMol ]
		FES	[ RasMol ]	+environment [ RasMol ]
		WMA	[ RasMol ]	+environment [ RasMol ]
		WMB	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1nip)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1nip
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	NIFH1_AZOVI \| P00459
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	NIFH1_AZOVI \| P00459
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Related Entries Specified in the PDB File" available for 1NIP)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 6)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (11, 11)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File