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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF (3R)-HYDROXYACYL-ACYL CARRIER PROTEIN DEHYDRATASE (FABZ) FROM HELICOBACTER PYLORI IN COMPLEX WITH COMPOUND 3J

Authors :   L. Zhang, L. He, X. Liu, H. Liu, X. Shen, H. Jiang

Date :   07 Jul 08 (Deposition) - 05 May 09 (Release) - 30 Jun 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym./Biol. Unit : A,B,C,D,E,F

Keywords :   Fabz Complex, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. He, L. Zhang, X. Liu, X. Li, M. Zheng, H. Li, K. Yu, K. Chen, X. Shen, H. Jiang, H. Liu
Discovering Potent Inhibitors Against The Beta-Hydroxyacyl-Acyl Carrier Protein Dehydratase (Fabz) Of Helicobacter Pylori: Structure-Based Design, Synthesis, Bioassay, And Crystal Structure Determination.
J. Med. Chem. V. 52 2465 2009
PubMed-ID: 19309082 | Reference-DOI: 10.1021/JM8015602
(for further references see the PDB file header)

Molecule 1 - (3R)-HYDROXYMYRISTOYL-ACYL CARRIER PROTEIN DEHYDRATASE
	Chains	:	A, B, C, D, E, F
	EC Number	:	4.2.1.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE30
	Expression System Strain	:	M15
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	FABZ
	Organism Common	:	CAMPYLOBACTER PYLORI
	Organism Scientific	:	HELICOBACTER PYLORI
	Organism Taxid	:	210
	Strain	:	SS1

		1	2	3	4	5	6
Asymmetric/Biological Unit	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 14)

No.	Name	Count	Type	Full Name
1	4BE	2	Ligand/Ion	4-BROMO-N'-[(1E)-(3,5-DIBROMO-2,4-DIHYDROXYPHENYL)METHYLIDENE]BENZOHYDRAZIDE
2	BEN	6	Ligand/Ion	BENZAMIDINE
3	CL	6	Ligand/Ion	CHLORIDE ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:58 , GLY A:67	BINDING SITE FOR RESIDUE CL A 160
02	AC2	SOFTWARE	HOH A:168 , HIS B:58 , GLY B:67 , HOH B:213	BINDING SITE FOR RESIDUE CL B 160
03	AC3	SOFTWARE	GLY C:67	BINDING SITE FOR RESIDUE CL C 160
04	AC4	SOFTWARE	HIS D:58 , GLY D:67 , HOH D:162	BINDING SITE FOR RESIDUE CL D 160
05	AC5	SOFTWARE	GLY E:67	BINDING SITE FOR RESIDUE CL E 160
06	AC6	SOFTWARE	HOH E:217 , GLY F:67	BINDING SITE FOR RESIDUE CL F 160
07	AC7	SOFTWARE	GLN A:40 , GLU A:124 , VAL A:125 , THR E:138 , GLU E:148 , BEN E:161	BINDING SITE FOR RESIDUE BEN A 161
08	AC8	SOFTWARE	MET A:154 , ILE A:155 , LEU F:86 , TRP F:87 , ASP F:90	BINDING SITE FOR RESIDUE BEN A 162
09	AC9	SOFTWARE	THR A:138 , GLU A:148 , HOH A:214 , GLU E:124 , VAL E:125 , LEU E:126 , BEN E:161 , HOH E:229	BINDING SITE FOR RESIDUE BEN A 163
10	BC1	SOFTWARE	TRP B:87 , GLY B:88 , HOH B:208 , LEU E:86 , GLY E:130 , MET E:131	BINDING SITE FOR RESIDUE BEN B 161
11	BC2	SOFTWARE	PHE A:59 , PHE A:109 , ARG A:110 , PRO A:112 , HOH A:199 , ILE B:98 , TYR B:100 , ARG B:158 , GLU B:159 , HOH B:188	BINDING SITE FOR RESIDUE 4BE B 162
12	BC3	SOFTWARE	LEU C:21 , PRO C:22 , HIS C:23 , GLY C:79 , ILE C:98 , VAL C:99 , PHE C:101 , HOH C:185 , HOH C:228 , PHE D:59	BINDING SITE FOR RESIDUE 4BE C 161
13	BC4	SOFTWARE	ALA C:38 , THR C:84 , SER C:85 , LEU C:86 , TRP C:87 , GLY C:88 , GLN D:40 , HOH D:217	BINDING SITE FOR RESIDUE BEN D 161
14	BC5	SOFTWARE	BEN A:161 , BEN A:163 , GLY E:136 , GLY E:137 , ALA E:149 , GLU E:150	BINDING SITE FOR RESIDUE BEN E 161

(no "SS Bond" information available for 3DP2)

Asymmetric/Biological Unit

No.	Residues
1	Tyr A:25	-	Pro A:26
2	His A:58	-	Phe A:59
3	Tyr B:25	-	Pro B:26
4	His B:58	-	Phe B:59
5	Tyr C:25	-	Pro C:26
6	His C:58	-	Phe C:59
7	Tyr D:25	-	Pro D:26
8	His D:58	-	Phe D:59
9	Tyr E:25	-	Pro E:26
10	His E:58	-	Phe E:59
11	Tyr F:25	-	Pro F:26
12	His F:58	-	Phe F:59

(no "SAP(SNP)/Variant" information available for 3DP2)

(no "PROSITE Motif" information available for 3DP2)

(no "Exon" information available for 3DP2)

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:152
 aligned with Q5G940_HELPX | Q5G940 from UniProtKB/TrEMBL  Length:159

    Alignment length:152
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157  
         Q5G940_HELPX     8 LQSQFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGHFPNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKVKFRIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAERE 159
               SCOP domains d3dp2a_ A: (3R)-hydroxymyristoyl ACP dehydrase FabZ                                                                                                      SCOP domains
               CATH domains 3dp2A00 A:8-159  [code=3.10.129.10, no name defined]                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh..........eeeeee...eeeeeee....hhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeeeeeeeeeeee........eeeeeeeeeeee..eeeeeeeeee..eeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dp2 A   8 LQSQFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGHFPNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKVKFRIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAERE 159
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157

Chain B from PDB  Type:PROTEIN  Length:150
 aligned with Q5G940_HELPX | Q5G940 from UniProtKB/TrEMBL  Length:159

    Alignment length:150
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159
         Q5G940_HELPX    10 SQFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGHFPNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKVKFRIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAERE 159
               SCOP domains d3dp2b_ B: (3R)-hydroxymyristoyl ACP dehydrase FabZ                                                                                                    SCOP domains
               CATH domains 3dp2B00 B:10-159  [code=3.10.129.10, no name defined]                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhh..........eeeeee...eeeeeee....hhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeeeeeeeeeeee........eeeeeeeeeeee..eeeeeeeeee..eeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3dp2 B  10 SQFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGHFPNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKVKFRIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAERE 159
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159

Chain C from PDB  Type:PROTEIN  Length:151
 aligned with Q5G940_HELPX | Q5G940 from UniProtKB/TrEMBL  Length:159

    Alignment length:151
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158 
         Q5G940_HELPX     9 QSQFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGHFPNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKVKFRIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAERE 159
               SCOP domains d3dp2c_ C: (3R)-hydroxymyristoyl ACP dehydrase FabZ                                                                                                     SCOP domains
               CATH domains 3dp2C00 C:9-159  [code=3.10.129.10, no name defined]                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh..........eeeeee...eeeeeee....hhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeeeeeeeeeeee........eeeeeeeeeeee..eeeeeeeeee..eeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dp2 C   9 QSQFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGHFPNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKVKFRIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAERE 159
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158

Chain D from PDB  Type:PROTEIN  Length:152
 aligned with Q5G940_HELPX | Q5G940 from UniProtKB/TrEMBL  Length:159

    Alignment length:152
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157  
         Q5G940_HELPX     8 LQSQFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGHFPNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKVKFRIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAERE 159
               SCOP domains d3dp2d_ D: (3R)-hydroxymyristoyl ACP dehydrase FabZ                                                                                                      SCOP domains
               CATH domains 3dp2D00 D:8-159  [code=3.10.129.10, no name defined]                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh..........eeeeee...eeeeeee....hhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeeeeeeeeeeee........eeeeeeeeeeee..eeeeeeeeee..eeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dp2 D   8 LQSQFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGHFPNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKVKFRIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAERE 159
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157

Chain E from PDB  Type:PROTEIN  Length:152
 aligned with Q5G940_HELPX | Q5G940 from UniProtKB/TrEMBL  Length:159

    Alignment length:152
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157  
         Q5G940_HELPX     8 LQSQFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGHFPNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKVKFRIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAERE 159
               SCOP domains d3dp2e_ E: (3R)-hydroxymyristoyl ACP dehydrase FabZ                                                                                                      SCOP domains
               CATH domains 3dp2E00 E:8-159  [code=3.10.129.10, no name defined]                                                                                                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eehhhhhhhh..........eeeeee...eeeeeee....hhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeeeeeeeeeeee........eeeeeeeeeeee..eeeeeeeeee..eeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dp2 E   8 LQSQFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGHFPNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKVKFRIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAERE 159
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157

Chain F from PDB  Type:PROTEIN  Length:148
 aligned with Q5G940_HELPX | Q5G940 from UniProtKB/TrEMBL  Length:159

    Alignment length:148
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150        
         Q5G940_HELPX    11 QFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGHFPNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKVKFRIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAER 158
               SCOP domains d3dp2f_ F: (3R)-hydroxymyristoyl ACP dehydrase FabZ                                                                                                  SCOP domains
               CATH domains 3dp2F00 F:11-158  [code=3.10.129.10, no name defined]                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh..........eeeeee...eeeeeee....hhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeeeeeeeeeeee........eeeeeeeeeeee..eeeeeeeeee..eeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dp2 F  11 QFFIEHILQILPHRYPMLLVDRITELQANQKIVAYKNITFNEDVFNGHFPNKPIFPGVLIVEGMAQSGGFLAFTSLWGFDPEIAKTKIVYFMTIDKVKFRIPVTPGDRLEYHLEVLKHKGMIWQVGGTAQVDGKVVAEAELKAMIAER 158
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150

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) (23004)

Fold: Thioesterase/thiol ester dehydrase-isomerase (151)

Superfamily: Thioesterase/thiol ester dehydrase-isomerase (151)

Family: FabZ-like (24)

Protein domain: (3R)-hydroxymyristoyl ACP dehydrase FabZ (24)

Helicobacter pylori [TaxId: 210] (15)

1a	d3dp2a_	A:
1b	d3dp2b_	B:
1c	d3dp2c_	C:
1d	d3dp2d_	D:
1e	d3dp2e_	E:
1f	d3dp2f_	F:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Thiol Ester Dehydrase; Chain A (90)

Homologous Superfamily: [code=3.10.129.10, no name defined] (90)

Campylobacter pylori (Helicobacter pylori) (7)

1a	3dp2F00	F:11-158
1b	3dp2B00	B:10-159
1c	3dp2C00	C:9-159
1d	3dp2A00	A:8-159
1e	3dp2D00	D:8-159
1f	3dp2E00	E:8-159

(no "Pfam Domain" information available for 3DP2)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D,E,F (Q5G940_HELPX | Q5G940)

molecular function
	GO:0019171	3-hydroxyacyl-[acyl-carrier-protein] dehydratase activity	Catalysis of the reaction: a (3R)-3-hydroxyacyl-[acyl-carrier protein] = H2O + a trans-delta2-enoyl-acyl-[acyl-carrier protein].
	GO:0047451	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity	Catalysis of the reaction: (3R)-3-hydroxyoctanoyl-[acyl-carrier protein] = H2O + 2-octenoyl-[acyl-carrier protein].
	GO:0016836	hydro-lyase activity	Catalysis of the cleavage of a carbon-oxygen bond by elimination of water.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
	GO:0006633	fatty acid biosynthetic process	The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
	GO:0009245	lipid A biosynthetic process	The chemical reactions and pathways resulting in the formation of lipid A, the glycolipid group of bacterial lipopolysaccharides, consisting of four to six fatty acyl chains linked to two glucosamine residues. Further modifications of the backbone are common.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		His A:58 - Phe A:59	[ RasMol ]
		His B:58 - Phe B:59	[ RasMol ]
		His C:58 - Phe C:59	[ RasMol ]
		His D:58 - Phe D:59	[ RasMol ]
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		Tyr E:25 - Pro E:26	[ RasMol ]
		Tyr F:25 - Pro F:26	[ RasMol ]

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	3dp2
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	Q5G940_HELPX \| Q5G940
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	4.2.1.-
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	Q5G940_HELPX \| Q5G940
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UniProtKB/Swiss-Prot
	Q5G940_HELPX \| Q5G940	:	2gll 2glm 2glp 2glv
UniProtKB/TrEMBL
	Q5G940_HELPX \| Q5G940	:	3b7j 3cf8 3cf9 3d04 3doy 3doz 3dp0 3dp1 3dp3 3ed0 4zjb

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 14)

Sites (14, 14)

SS Bonds (0, 0)

Cis Peptide Bonds (12, 12)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 6)

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Gene Ontology (8, 8)

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