3H3X - 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 :   STRUCTURE OF THE V74M LARGE SUBUNIT MUTANT OF NI-FE HYDROGENASE IN AN OXIDIZED STATE

Authors :   A. Volbeda, N. Martinez, L. Martin, J. C. Fontecilla-Camps

Date :   17 Apr 09 (Deposition) - 21 Jul 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Ni-Fe Hydrogenase Tunnel Mutant, Nickel, Iron, Oxidoreductase, Iron- Sulfur, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Dementin, F. Leroux, L. Cournac, A. L. De Lacey, A. Volbeda, C. Leger, B. Burlat, N. Martinez, S. Champ, L. Martin, O. Sanganas, M. Haumann, V. M. Fernandez, B. Guigliarelli, J. C. Fontecilla-Camps M. Rousset
Introduction Of Methionines In The Gas Channel Makes [Nife] Hydrogenase Aero-Tolerant
J. Am. Chem. Soc. V. 131 10156 2009
PubMed-ID: 19580279 | Reference-DOI: 10.1021/JA9018258
(for further references see the PDB file header)

Molecule 1 - PERIPLASMIC [NIFE] HYDROGENASE SMALL SUBUNIT
	Chains	:	A, B, C
	EC Number	:	1.12.2.1
	Engineered	:	YES
	Expression System	:	DESULFOVIBRIO FRUCTOSOVORANS
	Expression System Taxid	:	878
	Gene	:	HYDA
	Organism Scientific	:	DESULFOVIBRIO FRUCTOSOVORANS
	Organism Taxid	:	878
	Strain	:	DSM 3604
	Synonym	:	NIFE HYDROGENLYASE SMALL CHAIN

Molecule 2 - PERIPLASMIC [NIFE] HYDROGENASE LARGE SUBUNIT
	Chains	:	Q, R, S
	EC Number	:	1.12.2.1
	Engineered	:	YES
	Expression System	:	DESULFOVIBRIO FRUCTOSOVORANS
	Expression System Taxid	:	878
	Gene	:	HYDB
	Mutation	:	YES
	Organism Scientific	:	DESULFOVIBRIO FRUCTOSOVORANS
	Organism Taxid	:	878
	Strain	:	DSM 3604
	Synonym	:	NIFE HYDROGENLYASE LARGE CHAIN

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	Q	R	S
Biological Unit 1 (1x)	:	A			Q
Biological Unit 2 (1x)	:		B			R
Biological Unit 3 (1x)	:			C			S

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (6, 25)

No.	Name	Count	Type	Full Name
1	F3S	3	Ligand/Ion	FE3-S4 CLUSTER
2	FCO	3	Ligand/Ion	CARBONMONOXIDE-(DICYANO) IRON
3	GOL	7	Ligand/Ion	GLYCEROL
4	MG	3	Ligand/Ion	MAGNESIUM ION
5	NI	3	Ligand/Ion	NICKEL (II) ION
6	SF4	6	Ligand/Ion	IRON/SULFUR CLUSTER

Biological Unit 1 (4, 7)

No.	Name	Count	Type	Full Name
1	F3S	1	Ligand/Ion	FE3-S4 CLUSTER
2	FCO	1	Ligand/Ion	CARBONMONOXIDE-(DICYANO) IRON
3	GOL	3	Ligand/Ion	GLYCEROL
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NI	-1	Ligand/Ion	NICKEL (II) ION
6	SF4	2	Ligand/Ion	IRON/SULFUR CLUSTER

Biological Unit 2 (4, 7)

No.	Name	Count	Type	Full Name
1	F3S	1	Ligand/Ion	FE3-S4 CLUSTER
2	FCO	1	Ligand/Ion	CARBONMONOXIDE-(DICYANO) IRON
3	GOL	3	Ligand/Ion	GLYCEROL
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NI	-1	Ligand/Ion	NICKEL (II) ION
6	SF4	2	Ligand/Ion	IRON/SULFUR CLUSTER

Biological Unit 3 (4, 5)

No.	Name	Count	Type	Full Name
1	F3S	1	Ligand/Ion	FE3-S4 CLUSTER
2	FCO	1	Ligand/Ion	CARBONMONOXIDE-(DICYANO) IRON
3	GOL	1	Ligand/Ion	GLYCEROL
4	MG	-1	Ligand/Ion	MAGNESIUM ION
5	NI	-1	Ligand/Ion	NICKEL (II) ION
6	SF4	2	Ligand/Ion	IRON/SULFUR CLUSTER

Asymmetric Unit (25, 25)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:184 , CYS A:187 , ARG A:189 , LEU A:190 , PHE A:193 , CYS A:212 , LEU A:213 , TYR A:214 , CYS A:218	BINDING SITE FOR RESIDUE SF4 A 265
02	AC2	SOFTWARE	ASN A:225 , CYS A:227 , PHE A:232 , TRP A:237 , CYS A:245 , LEU A:246 , CYS A:248 , LYS Q:225 , GLN Q:230	BINDING SITE FOR RESIDUE F3S A 266
03	AC3	SOFTWARE	GLU A:16 , CYS A:17 , CYS A:20 , THR A:113 , CYS A:114 , GLY A:146 , CYS A:147 , PRO A:148 , ARG Q:70 , HIS Q:228	BINDING SITE FOR RESIDUE SF4 A 267
04	AC4	SOFTWARE	ASP A:168 , LEU A:169 , LYS A:176 , HOH A:322	BINDING SITE FOR RESIDUE GOL A 271
05	AC5	SOFTWARE	CYS Q:75 , VAL Q:78 , HIS Q:79 , ALA Q:474 , PRO Q:475 , ARG Q:476 , VAL Q:497 , PRO Q:498 , SER Q:499 , CYS Q:546 , NI Q:551	BINDING SITE FOR RESIDUE FCO Q 550
06	AC6	SOFTWARE	CYS Q:72 , CYS Q:75 , CYS Q:543 , CYS Q:546 , FCO Q:550	BINDING SITE FOR RESIDUE NI Q 551
07	AC7	SOFTWARE	GLU Q:53 , LEU Q:495 , HIS Q:549 , HOH Q:554 , HOH Q:555 , HOH Q:556	BINDING SITE FOR RESIDUE MG Q 553
08	AC8	SOFTWARE	ARG Q:100 , ASN Q:104 , PHE Q:295 , ALA Q:296 , THR Q:297 , TRP Q:442 , GLU Q:445	BINDING SITE FOR RESIDUE GOL Q 561
09	AC9	SOFTWARE	PHE C:198 , ASN Q:181 , ALA Q:182 , LEU Q:185 , ARG Q:529	BINDING SITE FOR RESIDUE GOL Q 562
10	BC1	SOFTWARE	HIS B:184 , CYS B:187 , ARG B:189 , LEU B:190 , CYS B:212 , LEU B:213 , TYR B:214 , CYS B:218 , PRO B:221	BINDING SITE FOR RESIDUE SF4 B 265
11	BC2	SOFTWARE	ASN B:225 , CYS B:227 , PHE B:232 , TRP B:237 , PRO B:238 , CYS B:245 , LEU B:246 , CYS B:248 , GLN R:230	BINDING SITE FOR RESIDUE F3S B 266
12	BC3	SOFTWARE	GLU B:16 , CYS B:17 , CYS B:20 , GLY B:112 , THR B:113 , CYS B:114 , GLY B:146 , CYS B:147 , PRO B:148 , HOH B:269 , ARG R:70	BINDING SITE FOR RESIDUE SF4 B 267
13	BC4	SOFTWARE	CYS R:75 , HIS R:79 , ALA R:474 , PRO R:475 , ARG R:476 , LEU R:479 , VAL R:497 , PRO R:498 , SER R:499 , CYS R:546 , NI R:551	BINDING SITE FOR RESIDUE FCO R 550
14	BC5	SOFTWARE	CYS R:72 , CYS R:75 , CYS R:543 , CYS R:546 , FCO R:550	BINDING SITE FOR RESIDUE NI R 551
15	BC6	SOFTWARE	GLU R:53 , LEU R:495 , HIS R:549 , HOH R:554 , HOH R:555 , HOH R:556	BINDING SITE FOR RESIDUE MG R 553
16	BC7	SOFTWARE	ALA B:55 , ASN R:181 , ALA R:182 , TYR R:183 , LEU R:185 , ARG R:529 , HOH R:670	BINDING SITE FOR RESIDUE GOL R 561
17	BC8	SOFTWARE	THR R:286 , SER R:287 , ASN R:288 , PRO R:514 , HOH R:630	BINDING SITE FOR RESIDUE GOL R 562
18	BC9	SOFTWARE	ARG R:100 , ASN R:104 , PHE R:295 , ALA R:296 , THR R:297 , GLN R:310 , GLU R:445 , HOH R:641	BINDING SITE FOR RESIDUE GOL R 563
19	CC1	SOFTWARE	HIS C:184 , CYS C:187 , LEU C:190 , CYS C:212 , LEU C:213 , CYS C:218 , PRO C:221	BINDING SITE FOR RESIDUE SF4 C 265
20	CC2	SOFTWARE	ASN C:225 , CYS C:227 , PHE C:232 , TRP C:237 , CYS C:245 , LEU C:246 , CYS C:248 , GLN S:230	BINDING SITE FOR RESIDUE F3S C 266
21	CC3	SOFTWARE	GLU C:16 , CYS C:17 , CYS C:20 , THR C:113 , CYS C:114 , GLY C:146 , CYS C:147 , ARG S:70	BINDING SITE FOR RESIDUE SF4 C 267
22	CC4	SOFTWARE	CYS S:75 , VAL S:78 , HIS S:79 , ALA S:474 , PRO S:475 , ARG S:476 , LEU S:479 , VAL S:497 , PRO S:498 , SER S:499 , CYS S:546 , NI S:551	BINDING SITE FOR RESIDUE FCO S 550
23	CC5	SOFTWARE	CYS S:72 , CYS S:75 , CYS S:543 , CYS S:546 , FCO S:550	BINDING SITE FOR RESIDUE NI S 551
24	CC6	SOFTWARE	GLU S:53 , LEU S:495 , HIS S:549 , HOH S:554 , HOH S:555 , HOH S:556	BINDING SITE FOR RESIDUE MG S 553
25	CC7	SOFTWARE	ARG S:100 , ASN S:104 , PHE S:295 , ALA S:296 , THR S:297 , TRP S:442 , GLU S:445	BINDING SITE FOR RESIDUE GOL S 561

Asymmetric Unit

No.	Residues
1	Q:72	-	Q:543
2	Q:75	-	Q:546
3	Q:259	-	Q:436
4	R:72	-	R:543
5	R:75	-	R:546
6	R:259	-	R:436
7	S:72	-	S:543
8	S:75	-	S:546
9	S:259	-	S:436

Asymmetric Unit

No.	Residues
1	Lys A:29	-	Pro A:30
2	Lys A:124	-	Pro A:125
3	Cys A:147	-	Pro A:148
4	Thr A:258	-	Pro A:259
5	Asp Q:19	-	Pro Q:20
6	Asn Q:226	-	Pro Q:227
7	Lys B:29	-	Pro B:30
8	Lys B:124	-	Pro B:125
9	Cys B:147	-	Pro B:148
10	Thr B:258	-	Pro B:259
11	Asp R:19	-	Pro R:20
12	Asn R:226	-	Pro R:227
13	Lys C:29	-	Pro C:30
14	Lys C:124	-	Pro C:125
15	Cys C:147	-	Pro C:148
16	Thr C:258	-	Pro C:259
17	Asp S:19	-	Pro S:20
18	Asn S:226	-	Pro S:227

(no "SAP(SNP)/Variant" information available for 3H3X)

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NI_HGENASE_L_1	PS00507	Nickel-dependent hydrogenases large subunit signature 1.	PHNL_DESFR	50-75	3	Q:50-75 R:50-75 S:50-75
2	NI_HGENASE_L_2	PS00508	Nickel-dependent hydrogenases large subunit signature 2.	PHNL_DESFR	540-549	3	Q:540-549 R:540-549 S:540-549

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NI_HGENASE_L_1	PS00507	Nickel-dependent hydrogenases large subunit signature 1.	PHNL_DESFR	50-75	1	Q:50-75 - -
2	NI_HGENASE_L_2	PS00508	Nickel-dependent hydrogenases large subunit signature 2.	PHNL_DESFR	540-549	1	Q:540-549 - -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NI_HGENASE_L_1	PS00507	Nickel-dependent hydrogenases large subunit signature 1.	PHNL_DESFR	50-75	1	- R:50-75 -
2	NI_HGENASE_L_2	PS00508	Nickel-dependent hydrogenases large subunit signature 2.	PHNL_DESFR	540-549	1	- R:540-549 -

Biological Unit 3 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	NI_HGENASE_L_1	PS00507	Nickel-dependent hydrogenases large subunit signature 1.	PHNL_DESFR	50-75	1	- - S:50-75
2	NI_HGENASE_L_2	PS00508	Nickel-dependent hydrogenases large subunit signature 2.	PHNL_DESFR	540-549	1	- - S:540-549

(no "Exon" information available for 3H3X)

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:262
 aligned with PHNS_DESFR | P18187 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:262
                                    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  
           PHNS_DESFR    53 AKHRPSVVWLHNAECTGCTEAAIRTIKPYIDALILDTISLDYQETIMAAAGEAAEAALHQALEGKDGYYLVVEGGLPTIDGGQWGMVAGHPMIETTKKAAAKAKGIICIGTCSAYGGVQKAKPNPSQAKGVSEALGVKTINIPGCPPNPINFVGAVVHVLTKGIPDLDENGRPKLFYGELVHDNCPRLPHFEASEFAPSFDSEEAKKGFCLYELGCKGPVTYNNCPKVLFNQVNWPVQAGHPCLGCSEPDFWDTMTPFYEQG 314
               SCOP domains d3h3xa_ A: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains 3h3xA01 A:3-178  [code=3.40.50.700, no name defined]                                                                                                                            3h3xA02 A:179-263 Cytochrome-c3 Hydrogenase, chain A, domain 2                       - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee....hhhhhhhh.....hhhhhhhhh.eeee.......hhhhhhhhhhhhhh.....eeeee..eehhhhhh..ee..eehhhhhhhhhhh...eeeehhhhhhhhhhhh......eehhhhhhh...eee.....hhhhhhhhhhhhhhh..........hhhhhh..hhhhh.hhhhhhh........hhhhhh...hhhhh.hhhhh..hhhhhh......hhhhh.........hhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h3x A   3 AKHRPSVVWLHNAECTGCTEAAIRTIKPYIDALILDTISLDYQETIMAAAGEAAEAALHQALEGKDGYYLVVEGGLPTIDGGQWGMVAGHPMIETTKKAAAKAKGIICIGTCSAYGGVQKAKPNPSQAKGVSEALGVKTINIPGCPPNPINFVGAVVHVLTKGIPDLDENGRPKLFYGELVHDNCPRLPHFEASEFAPSFDSEEAKKGFCLYELGCKGPVTYNNCPKVLFNQVNWPVQAGHPCLGCSEPDFWDTMTPFYEQG 264
                                    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

Chain B from PDB  Type:PROTEIN  Length:262
 aligned with PHNS_DESFR | P18187 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:262
                                    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  
           PHNS_DESFR    53 AKHRPSVVWLHNAECTGCTEAAIRTIKPYIDALILDTISLDYQETIMAAAGEAAEAALHQALEGKDGYYLVVEGGLPTIDGGQWGMVAGHPMIETTKKAAAKAKGIICIGTCSAYGGVQKAKPNPSQAKGVSEALGVKTINIPGCPPNPINFVGAVVHVLTKGIPDLDENGRPKLFYGELVHDNCPRLPHFEASEFAPSFDSEEAKKGFCLYELGCKGPVTYNNCPKVLFNQVNWPVQAGHPCLGCSEPDFWDTMTPFYEQG 314
               SCOP domains d3h3xb_ B: automated matches                                                                                                                                                                                                                                           SCOP domains
               CATH domains 3h3xB01 B:3-178  [code=3.40.50.700, no name defined]                                                                                                                            3h3xB02 B:179-263 Cytochrome-c3 Hydrogenase, chain A, domain 2                       - CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee....hhhhhhhh.....hhhhhhhhh.eeee.......hhhhhhhhhhhhhh.....eeeee..eehhhhhh..ee..eehhhhhhhhhhh...eeeehhhhhhhhhhhh......eehhhhhhh...eee.....hhhhhhhhhhhhhhh..........hhhhhh..hhhhh.hhhhhhh........hhhhhh...hhhhh.hhhhh..hhhhhh....................hhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h3x B   3 AKHRPSVVWLHNAECTGCTEAAIRTIKPYIDALILDTISLDYQETIMAAAGEAAEAALHQALEGKDGYYLVVEGGLPTIDGGQWGMVAGHPMIETTKKAAAKAKGIICIGTCSAYGGVQKAKPNPSQAKGVSEALGVKTINIPGCPPNPINFVGAVVHVLTKGIPDLDENGRPKLFYGELVHDNCPRLPHFEASEFAPSFDSEEAKKGFCLYELGCKGPVTYNNCPKVLFNQVNWPVQAGHPCLGCSEPDFWDTMTPFYEQG 264
                                    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

Chain C from PDB  Type:PROTEIN  Length:260
 aligned with PHNS_DESFR | P18187 from UniProtKB/Swiss-Prot  Length:314

    Alignment length:260
                                    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
           PHNS_DESFR    55 HRPSVVWLHNAECTGCTEAAIRTIKPYIDALILDTISLDYQETIMAAAGEAAEAALHQALEGKDGYYLVVEGGLPTIDGGQWGMVAGHPMIETTKKAAAKAKGIICIGTCSAYGGVQKAKPNPSQAKGVSEALGVKTINIPGCPPNPINFVGAVVHVLTKGIPDLDENGRPKLFYGELVHDNCPRLPHFEASEFAPSFDSEEAKKGFCLYELGCKGPVTYNNCPKVLFNQVNWPVQAGHPCLGCSEPDFWDTMTPFYEQG 314
               SCOP domains d3h3xc_ C: automated matches                                                                                                                                                                                                                                         SCOP domains
               CATH domains 3h3xC01 C:5-178  [code=3.40.50.700, no name defined]                                                                                                                          3h3xC02 C:179-263 Cytochrome-c3 Hydrogenase, chain A, domain 2                       - CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee....hhhhhhhh.....hhhhhhhhh.eeee.......hhhhhhhhhhhhhh.....eeeee..ee.hhhhh..ee..eehhhhhhhhhhh...eeeehhhhhhhhhhhh......eehhhhhhh...eee.....hhhhhhhhhhhhhhh..........hhhhhh..hhhhh.hhhhhhhh.......hhhhhh...hhhhh.hhhhh..hhhhhh....................hhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h3x C   5 HRPSVVWLHNAECTGCTEAAIRTIKPYIDALILDTISLDYQETIMAAAGEAAEAALHQALEGKDGYYLVVEGGLPTIDGGQWGMVAGHPMIETTKKAAAKAKGIICIGTCSAYGGVQKAKPNPSQAKGVSEALGVKTINIPGCPPNPINFVGAVVHVLTKGIPDLDENGRPKLFYGELVHDNCPRLPHFEASEFAPSFDSEEAKKGFCLYELGCKGPVTYNNCPKVLFNQVNWPVQAGHPCLGCSEPDFWDTMTPFYEQG 264
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264

Chain Q from PDB  Type:PROTEIN  Length:544
 aligned with PHNL_DESFR | P18188 from UniProtKB/Swiss-Prot  Length:564

    Alignment length:544
                                    15        25        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       525       535       545    
           PHNL_DESFR     6 PTPQSTFTGPIVVDPITRIEGHLRIMVEVENGKVKDAWSSSQLFRGLEIILKGRDPRDAQHFTQRACGVCTYVHALASSRCVDDAVKVSIPANARMMRNLVMASQYLHDHLVHFYHLHALDWVDVTAALKADPNKAAKLAASIAPARPGNSAKALKAVQDKLKAFVESGQLGIFTNAYFLGGHKAYYLPPEVDLIATAHYLEALHMQVKAASAMAILGGKNPHTQFTVVGGCSNYQGLTKDPLANYLALSKEVCQFVNECYIPDLLAVAGFYKDWGGIGGTSNYLAFGEFATDDSSPEKHLATSQFPSGVITGRDLGKVDNVDLGAIYEDVKYSWYAPGGDGKHPYDGVTDPKYTKLDDKDHYSWMKAPRYKGKAMEVGPLARTFIAYAKGQPDFKKVVDMVLGKLSVPATALHSTLGRTAARGIETAIVCANMEKWIKEMADSGAKDNTLCAKWEMPEESKGVGLADAPRGALSHWIRIKGKKIDNFQLVVPSTWNLGPRGAQGDKSPVEEALIGTPIADPKRPVEILRTVHAFDPCIACGVH 549
               SCOP domains d3h3xq_ Q: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 3h3xQ00 Q:6-549 Cytochrome-c3 Hydrogenase, chain B                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee.........eeeeeeee..eeeeeeeee....hhhhhhh..hhhhhhhhhhh......hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..hhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......ee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee..eee....hhhhhhhheee..eee...........hhh.eeee.............hhhhh...................eeee.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeeeeeeeee..eeeeeeeeee..eeeeeeeehhhhhhhh........hhhhhhhh.........hhhhhhhhhhh..hhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------NI_HGENASE_L_1            --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NI_HGENASE PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h3x Q   6 PTPQSTFTGPIVVDPITRIEGHLRIMVEVENGKVKDAWSSSQLFRGLEIILKGRDPRDAQHFTQRACGMCTYVHALASSRCVDDAVKVSIPANARMMRNLVMASQYLHDHLVHFYHLHALDWVDVTAALKADPNKAAKLAASIAPARPGNSAKALKAVQDKLKAFVESGQLGIFTNAYFLGGHKAYYLPPEVDLIATAHYLEALHMQVKAASAMAILGGKNPHTQFTVVGGCSNYQGLTKDPLANYLALSKEVCQFVNECYIPDLLAVAGFYKDWGGIGGTSNYLAFGEFATDDSSPEKHLATSQFPSGVITGRDLGKVDNVDLGAIYEDVKYSWYAPGGDGKHPYDGVTDPKYTKLDDKDHYSWMKAPRYKGKAMEVGPLARTFIAYAKGQPDFKKVVDMVLGKLSVPATALHSTLGRTAARGIETAIVCANMEKWIKEMADSGAKDNTLCAKWEMPEESKGVGLADAPRGALSHWIRIKGKKIDNFQLVVPSTWNLGPRGAQGDKSPVEEALIGTPIADPKRPVEILRTVHAFDPCIACGVH 549
                                    15        25        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       525       535       545

Chain R from PDB  Type:PROTEIN  Length:545
 aligned with PHNL_DESFR | P18188 from UniProtKB/Swiss-Prot  Length:564

    Alignment length:545
                                    14        24        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       524       534       544     
           PHNL_DESFR     5 KPTPQSTFTGPIVVDPITRIEGHLRIMVEVENGKVKDAWSSSQLFRGLEIILKGRDPRDAQHFTQRACGVCTYVHALASSRCVDDAVKVSIPANARMMRNLVMASQYLHDHLVHFYHLHALDWVDVTAALKADPNKAAKLAASIAPARPGNSAKALKAVQDKLKAFVESGQLGIFTNAYFLGGHKAYYLPPEVDLIATAHYLEALHMQVKAASAMAILGGKNPHTQFTVVGGCSNYQGLTKDPLANYLALSKEVCQFVNECYIPDLLAVAGFYKDWGGIGGTSNYLAFGEFATDDSSPEKHLATSQFPSGVITGRDLGKVDNVDLGAIYEDVKYSWYAPGGDGKHPYDGVTDPKYTKLDDKDHYSWMKAPRYKGKAMEVGPLARTFIAYAKGQPDFKKVVDMVLGKLSVPATALHSTLGRTAARGIETAIVCANMEKWIKEMADSGAKDNTLCAKWEMPEESKGVGLADAPRGALSHWIRIKGKKIDNFQLVVPSTWNLGPRGAQGDKSPVEEALIGTPIADPKRPVEILRTVHAFDPCIACGVH 549
               SCOP domains d3h3xr_ R: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 3h3xR00 R:5-549 Cytochrome-c3 Hydrogenase, chain B                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee.........eeeeeeee..eeeeeeeee....hhhhhhh..hhhhhhhhhhhhh....hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh..hhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......ee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee..eee....hhhhhhhheee..eee...........hhh.eeee.............hhhhh...................eeee.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeeeeeeeee..eeeeeeeeee..eeeeeeeehhhhhhhh........hhhhhhhh.........hhhhhhhhhhh..hhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------NI_HGENASE_L_1            --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NI_HGENASE PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h3x R   5 KPTPQSTFTGPIVVDPITRIEGHLRIMVEVENGKVKDAWSSSQLFRGLEIILKGRDPRDAQHFTQRACGMCTYVHALASSRCVDDAVKVSIPANARMMRNLVMASQYLHDHLVHFYHLHALDWVDVTAALKADPNKAAKLAASIAPARPGNSAKALKAVQDKLKAFVESGQLGIFTNAYFLGGHKAYYLPPEVDLIATAHYLEALHMQVKAASAMAILGGKNPHTQFTVVGGCSNYQGLTKDPLANYLALSKEVCQFVNECYIPDLLAVAGFYKDWGGIGGTSNYLAFGEFATDDSSPEKHLATSQFPSGVITGRDLGKVDNVDLGAIYEDVKYSWYAPGGDGKHPYDGVTDPKYTKLDDKDHYSWMKAPRYKGKAMEVGPLARTFIAYAKGQPDFKKVVDMVLGKLSVPATALHSTLGRTAARGIETAIVCANMEKWIKEMADSGAKDNTLCAKWEMPEESKGVGLADAPRGALSHWIRIKGKKIDNFQLVVPSTWNLGPRGAQGDKSPVEEALIGTPIADPKRPVEILRTVHAFDPCIACGVH 549
                                    14        24        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       524       534       544

Chain S from PDB  Type:PROTEIN  Length:544
 aligned with PHNL_DESFR | P18188 from UniProtKB/Swiss-Prot  Length:564

    Alignment length:544
                                    15        25        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       525       535       545    
           PHNL_DESFR     6 PTPQSTFTGPIVVDPITRIEGHLRIMVEVENGKVKDAWSSSQLFRGLEIILKGRDPRDAQHFTQRACGVCTYVHALASSRCVDDAVKVSIPANARMMRNLVMASQYLHDHLVHFYHLHALDWVDVTAALKADPNKAAKLAASIAPARPGNSAKALKAVQDKLKAFVESGQLGIFTNAYFLGGHKAYYLPPEVDLIATAHYLEALHMQVKAASAMAILGGKNPHTQFTVVGGCSNYQGLTKDPLANYLALSKEVCQFVNECYIPDLLAVAGFYKDWGGIGGTSNYLAFGEFATDDSSPEKHLATSQFPSGVITGRDLGKVDNVDLGAIYEDVKYSWYAPGGDGKHPYDGVTDPKYTKLDDKDHYSWMKAPRYKGKAMEVGPLARTFIAYAKGQPDFKKVVDMVLGKLSVPATALHSTLGRTAARGIETAIVCANMEKWIKEMADSGAKDNTLCAKWEMPEESKGVGLADAPRGALSHWIRIKGKKIDNFQLVVPSTWNLGPRGAQGDKSPVEEALIGTPIADPKRPVEILRTVHAFDPCIACGVH 549
               SCOP domains d3h3xs_ S: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 3h3xS00 S:6-549 Cytochrome-c3 Hydrogenase, chain B                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee.........eeeeeeee..eeeeeeeee....hhhhhhh..hhhhhhhhhhh......hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..hhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......ee..ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee..eee....hhhhhhhheee..eee...........hhh.eeee.............hhhhh...................eeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeeeeeeeee..eeeeeeeeee..eeeeeeeehhhhhhhh........hhhhhhhh.........hhhhhhhhhhh..hhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------NI_HGENASE_L_1            --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------NI_HGENASE PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3h3x S   6 PTPQSTFTGPIVVDPITRIEGHLRIMVEVENGKVKDAWSSSQLFRGLEIILKGRDPRDAQHFTQRACGMCTYVHALASSRCVDDAVKVSIPANARMMRNLVMASQYLHDHLVHFYHLHALDWVDVTAALKADPNKAAKLAASIAPARPGNSAKALKAVQDKLKAFVESGQLGIFTNAYFLGGHKAYYLPPEVDLIATAHYLEALHMQVKAASAMAILGGKNPHTQFTVVGGCSNYQGLTKDPLANYLALSKEVCQFVNECYIPDLLAVAGFYKDWGGIGGTSNYLAFGEFATDDSSPEKHLATSQFPSGVITGRDLGKVDNVDLGAIYEDVKYSWYAPGGDGKHPYDGVTDPKYTKLDDKDHYSWMKAPRYKGKAMEVGPLARTFIAYAKGQPDFKKVVDMVLGKLSVPATALHSTLGRTAARGIETAIVCANMEKWIKEMADSGAKDNTLCAKWEMPEESKGVGLADAPRGALSHWIRIKGKKIDNFQLVVPSTWNLGPRGAQGDKSPVEEALIGTPIADPKRPVEILRTVHAFDPCIACGVH 549
                                    15        25        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       525       535       545

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 "Pfam Domain" information available for 3H3X)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (PHNS_DESFR | P18187)

molecular function
	GO:0051538	3 iron, 4 sulfur cluster binding	Interacting selectively and non-covalently with a 3 iron, 4 sulfur (3Fe-4S) cluster; this cluster consists of three iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. It is essentially a 4Fe-4S cluster with one iron missing.
	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:0047806	cytochrome-c3 hydrogenase activity	Catalysis of the reaction: 2 H2 + ferricytochrome c3 = 4 H+ + ferrocytochrome c3.
	GO:0008901	ferredoxin hydrogenase activity	Catalysis of the reaction: 2 reduced ferredoxin + 2 H+ = 2 oxidized ferredoxin + H2.
	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: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: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:0009375	ferredoxin hydrogenase complex	An enzyme complex that catalyzes the oxidation of reduced ferredoxin. Hydrogenase contains iron-sulfur clusters, and some contain nickel; it can use molecular hydrogen for the reduction of a variety of substances.
	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).

Chain Q,R,S (PHNL_DESFR | P18188)

molecular function
	GO:0047806	cytochrome-c3 hydrogenase activity	Catalysis of the reaction: 2 H2 + ferricytochrome c3 = 4 H+ + ferrocytochrome c3.
	GO:0008901	ferredoxin hydrogenase activity	Catalysis of the reaction: 2 reduced ferredoxin + 2 H+ = 2 oxidized ferredoxin + H2.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016151	nickel cation binding	Interacting selectively and non-covalently with nickel (Ni) cations.
	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: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: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).

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	Cis Peptide Bonds
		Asn Q:226 - Pro Q:227	[ RasMol ]
		Asn R:226 - Pro R:227	[ RasMol ]
		Asn S:226 - Pro S:227	[ RasMol ]
		Asp Q:19 - Pro Q:20	[ RasMol ]
		Asp R:19 - Pro R:20	[ RasMol ]
		Asp S:19 - Pro S:20	[ RasMol ]
		Cys A:147 - Pro A:148	[ RasMol ]
		Cys B:147 - Pro B:148	[ RasMol ]
		Cys C:147 - Pro C:148	[ RasMol ]
		Lys A:124 - Pro A:125	[ RasMol ]
		Lys A:29 - Pro A:30	[ RasMol ]
		Lys B:124 - Pro B:125	[ RasMol ]
		Lys B:29 - Pro B:30	[ RasMol ]
		Lys C:124 - Pro C:125	[ RasMol ]
		Lys C:29 - Pro C:30	[ RasMol ]
		Thr A:258 - Pro A:259	[ RasMol ]
		Thr B:258 - Pro B:259	[ RasMol ]
		Thr C:258 - Pro C:259	[ RasMol ]

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	3h3x
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	PHNS_DESFR \| P18187
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	1.12.2.1
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1frf	STRUCTURE OF THE NATIVE ENZYME REFINED AT 2.7 ANGSTROM
1yqw	STRUCTURE OF THE OXIDISED UNREADY FORM OF THE NATIVE ENZYME REFINED AT 1.8 ANGSTROM RESOLUTION
1yrq	STRUCTURE OF THE OXIDISED READY FORM OF THE NATIVE ENZYME REFINED AT 2.1 ANGSTROM RESOLUTION
3cur	STRUCTURE OF A DOUBLE METHIONINE MUTANT REFINED AT 2.4 ANGSTROM RESOLUTION
3cus	STRUCTURE OF A DOUBLE ILE/PHE MUTANT REFINED AT 2.2 ANGSTROM RESOLUTION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 25)

Sites (25, 25)

SS Bonds (9, 9)

Cis Peptide Bonds (18, 18)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 6)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 6)

CATH Domains (3, 9)

Pfam Domains (0, 0)

Gene Ontology (11, 17)

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