4E5Y - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF HUMAN FX PROTEIN, THE KEY ENZYME IN THE BIOSYNTHESIS OF GDP-L-FUCOSE

Authors :   H. Zhou, J. H. He

Date :   15 Mar 12 (Deposition) - 17 Apr 13 (Release) - 17 Apr 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.37

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

Keywords :   Biosynthesis, Gdp-L-Fucose, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Zhou, J. H. He
Structure Of Human Fx Protein, The Key Enzyme In The Biosynthesis Of Gdp-L-Fucose
To Be Published
PubMed: search

Molecule 1 - GDP-L-FUCOSE SYNTHASE
	Chains	:	A, B, C, D
	EC Number	:	1.1.1.271
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	TSTA3, SDR4E1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	GDP-4-KETO-6-DEOXY-D-MANNOSE-3,5-EPIMERASE-4-REDUCTASE, PROTEIN FX, RED CELL NADP(H)-BINDING PROTEIN, SHORT-CHAIN DEHYDROGENASE/REDUCTASE FAMILY 4E MEMBER 1

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	NDP	4	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	NDP	2	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	NDP	2	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:14 , SER A:16 , GLY A:17 , LEU A:18 , VAL A:19 , SER A:42 , SER A:43 , ALA A:46 , ASP A:47 , LEU A:48 , LEU A:69 , ALA A:70 , ALA A:71 , CYS A:112 , LEU A:113 , SER A:114 , TYR A:143 , LYS A:147 , PRO A:170 , THR A:171 , VAL A:173 , ARG A:320	BINDING SITE FOR RESIDUE NDP A 401
2	AC2	SOFTWARE	GLY B:14 , SER B:16 , GLY B:17 , LEU B:18 , VAL B:19 , SER B:42 , SER B:43 , LYS B:44 , ALA B:46 , ASP B:47 , LEU B:48 , LEU B:69 , ALA B:70 , ALA B:71 , VAL B:73 , CYS B:112 , LEU B:113 , SER B:114 , TYR B:143 , LYS B:147 , PRO B:170 , THR B:171 , VAL B:173 , ARG B:320	BINDING SITE FOR RESIDUE NDP B 401
3	AC3	SOFTWARE	GLY C:14 , SER C:16 , GLY C:17 , LEU C:18 , VAL C:19 , SER C:42 , SER C:43 , ALA C:46 , ASP C:47 , LEU C:48 , LEU C:69 , ALA C:70 , ALA C:71 , VAL C:73 , MET C:93 , CYS C:112 , LEU C:113 , SER C:114 , TYR C:143 , LYS C:147 , THR C:171 , VAL C:173 , HIS C:186 , ARG C:320	BINDING SITE FOR RESIDUE NDP C 401
4	AC4	SOFTWARE	GLY D:14 , SER D:16 , GLY D:17 , LEU D:18 , VAL D:19 , SER D:42 , SER D:43 , ALA D:46 , ASP D:47 , LEU D:48 , LEU D:69 , ALA D:70 , ALA D:71 , CYS D:112 , LEU D:113 , SER D:114 , TYR D:143 , LYS D:147 , PRO D:170 , THR D:171 , ASN D:172 , VAL D:173 , ARG D:320 , HOH D:502	BINDING SITE FOR RESIDUE NDP D 401

(no "SS Bond" information available for 4E5Y)

Asymmetric Unit

No.	Residues
1	Lys A:25	-	Val A:26
2	Val A:27	-	Ala A:28
3	Ser A:43	-	Lys A:44
4	Tyr A:124	-	Pro A:125
5	Leu A:205	-	Thr A:206
6	Gln A:279	-	Phe A:280
7	Lys B:25	-	Val B:26
8	Val B:27	-	Ala B:28
9	Ser B:42	-	Ser B:43
10	Tyr B:124	-	Pro B:125
11	Leu B:205	-	Thr B:206
12	Thr B:206	-	Val B:207
13	Gln B:279	-	Phe B:280
14	Lys C:25	-	Val C:26
15	Val C:27	-	Ala C:28
16	Ser C:42	-	Ser C:43
17	Lys C:44	-	Asp C:45
18	Val C:73	-	Gly C:74
19	Tyr C:124	-	Pro C:125
20	Leu C:191	-	Ile C:192
21	Gly C:202	-	Ser C:203
22	Ser C:203	-	Ala C:204
23	Pro C:213	-	Arg C:214
24	Arg C:214	-	Arg C:215
25	Val C:250	-	Ser C:251
26	Val C:259	-	Val C:260
27	Lys C:275	-	Ser C:276
28	Gly C:278	-	Gln C:279
29	Gln D:5	-	Gly D:6
30	Lys D:25	-	Val D:26
31	Val D:27	-	Ala D:28
32	Gly D:32	-	Leu D:33
33	Leu D:33	-	Pro D:34
34	Ser D:43	-	Lys D:44
35	Tyr D:124	-	Pro D:125
36	Leu D:205	-	Thr D:206
37	Thr D:206	-	Val D:207
38	Gln D:279	-	Phe D:280

(no "SAP(SNP)/Variant" information available for 4E5Y)

(no "PROSITE Motif" information available for 4E5Y)

(no "Exon" information available for 4E5Y)

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:307
                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4e5ya_ A: automated matches                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhh.........eeee.........hhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh........hhhhh........hhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.eee...........hhhhhhhhhhhhhhh.............ee.eeehhhhhhhhhhhhhh......eee.......eehhhhhhhhhhhhh................hhhhhhhh......hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e5y A   7 SMRILVTGGSGLVGKAIQKVVADGAGEDWVFVSSKDADLTDTAQTRALFEKVQPTHVIHLAAMVGGLFRNIKYNLDFWRKNVHMNDNVLHSAFEVGARKVVSCLSTCIFPDKTTYPIDETMIHNGPPHNSNFGYSYAKRMIDVQNRAYFQQYGCTFTAVIPTNVFGPHDNFNIEDGHVLPGLIHKVHLAKSSGSALTVWGTGNPRRQFIYSLDLAQLFIWVLREYNEVEPIILSVGEEDEVSIKEAAEAVVEAMDFHGEVTFDGQFKKTASNSKLRTYLPDFRFTPFKQAVKETCAWFTDNYEQARK 321
                                    16        26     || 39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269  ||   284       294       304       314       
                                                    32|                                                                                                                                                                                                                                         272|                                           
                                                     36                                                                                                                                                                                                                                          278

Chain B from PDB  Type:PROTEIN  Length:309
                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains d4e5yb_ B: automated matches                                                                                                                                                                                                                                                                                          SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...hhhhhhhh..........eee.........hhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh........hhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.eee...........hhhhhhhhhhhhhhh............ee.eeehhhhhhhhhhhhhh......eee.......eehhhhhhhhhhhh....................hhhhhhhh......hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e5y B   7 SMRILVTGGSGLVGKAIQKVVADGAGEDWVFVSSKDADLTDTAQTRALFEKVQPTHVIHLAAMVGGLFRNIKYNLDFWRKNVHMNDNVLHSAFEVGARKVVSCLSTCIFPDKTTYPIDETMIHNGPPHNSNFGYSYAKRMIDVQNRAYFQQYGCTFTAVIPTNVFGPHDNFNIEDGHVLPGLIHKVHLAKSSGSLTVWGTGNPRRQFIYSLDLAQLFIWVLREYNEVEPIILSVGEEDEVSIKEAAEAVVEAMDFHGVTFDTTKSDQFKKTASNSKLRTYLPDFRFTPFKQAVKETCAWFTDNYEQARK 321
                                    16        26     || 39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199   ||  210       220       230       240       250       260      |271     ||282       292       302       312         
                                                    32|                                                                                                                                                                    203|                                                           267|     277|                                          
                                                     36                                                                                                                                                                     205                                                            269      279

Chain C from PDB  Type:PROTEIN  Length:290
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4e5yc_ C: automated matches                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhhhhh.........eeee.........hhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh........hhhhh........hhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.eee..................................eeehhhhhhhhhhhhhhh.....eee...................................hhhhhhhh......hhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4e5y C   7 SMRILVTGGSGLVGKAIQKVVADGAGEDWVFVSSKDADLTDTAQTRALFEKVQPTHVIHLAAMVGKYNLDFWRKNVHMNDNVLHSAFEVGARKVVSCLSTCIFPDKTTYPIDETMIHNGPPHNSNFGYSYAKRMIDVQNRAYFQQYGCTFTAVIPTNVFGPHDNFNIEDGHVLPGLIHGSALTVWGTGNPRRQFIYSLDLAQLFIWVLREYNEVEPIILSVGEEDEVSIKEAAEAVVEAMDTTKSDGQFKKTASNSKLRTYLPDFRFTPFKQAVKETCAWFTDNYEQARK 321
                                    16        26     || 39        49        59        69    ||  85        95       105       115       125       135       145       155       165       175       185       203       213       223       233       243       253       263|      281       291       301       311       321
                                                    32|                                    74|                                                                                                             193|                                                          263|                                                 
                                                     36                                     81                                                                                                              202                                                           272

Chain D from PDB  Type:PROTEIN  Length:318
                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4e5yd_ D: automated matches                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eeee...hhhhhhhh.............eee.........hhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh........hhhhh........hhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.eee...........hhhhhhhhhhhhhhh.............ee.eeehhhhhhhhhhhhhh......eee.......eehhhhhhhhhhhhh.....................hhhhhhhh......hhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4e5y D   4 PQGSMRILVTGGSGLVGKAIQKVVADGAGLPGEDWVFVSSKDADLTDTAQTRALFEKVQPTHVIHLAAMVGGLFRNIKYNLDFWRKNVHMNDNVLHSAFEVGARKVVSCLSTCIFPDKTTYPIDETMIHNGPPHNSNFGYSYAKRMIDVQNRAYFQQYGCTFTAVIPTNVFGPHDNFNIEDGHVLPGLIHKVHLAKSSGSALTVWGTGNPRRQFIYSLDLAQLFIWVLREYNEVEPIILSVGEEDEVSIKEAAEAVVEAMDFHGEVTFDTTKSDGQFKKTASNSKLRTYLPDFRFTPFKQAVKETCAWFTDNYEQARK 321
                                    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

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: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: automated matches (447)

Protein domain: automated matches (447)

Human (Homo sapiens) [TaxId: 9606] (32)

1a	d4e5ya_	A:
1b	d4e5yb_	B:
1c	d4e5yc_	C:
1d	d4e5yd_	D:

(no "CATH Domain" information available for 4E5Y)

(no "Pfam Domain" information available for 4E5Y)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Arg C:214 - Arg C:215	[ RasMol ]
		Gln A:279 - Phe A:280	[ RasMol ]
		Gln B:279 - Phe B:280	[ RasMol ]
		Gln D:279 - Phe D:280	[ RasMol ]
		Gln D:5 - Gly D:6	[ RasMol ]
		Gly C:202 - Ser C:203	[ RasMol ]
		Gly C:278 - Gln C:279	[ RasMol ]
		Gly D:32 - Leu D:33	[ RasMol ]
		Leu A:205 - Thr A:206	[ RasMol ]
		Leu B:205 - Thr B:206	[ RasMol ]
		Leu C:191 - Ile C:192	[ RasMol ]
		Leu D:205 - Thr D:206	[ RasMol ]
		Leu D:33 - Pro D:34	[ RasMol ]
		Lys A:25 - Val A:26	[ RasMol ]
		Lys B:25 - Val B:26	[ RasMol ]
		Lys C:25 - Val C:26	[ RasMol ]
		Lys C:275 - Ser C:276	[ RasMol ]
		Lys C:44 - Asp C:45	[ RasMol ]
		Lys D:25 - Val D:26	[ RasMol ]
		Pro C:213 - Arg C:214	[ RasMol ]
		Ser A:43 - Lys A:44	[ RasMol ]
		Ser B:42 - Ser B:43	[ RasMol ]
		Ser C:203 - Ala C:204	[ RasMol ]
		Ser C:42 - Ser C:43	[ RasMol ]
		Ser D:43 - Lys D:44	[ RasMol ]
		Thr B:206 - Val B:207	[ RasMol ]
		Thr D:206 - Val D:207	[ RasMol ]
		Tyr A:124 - Pro A:125	[ RasMol ]
		Tyr B:124 - Pro B:125	[ RasMol ]
		Tyr C:124 - Pro C:125	[ RasMol ]
		Tyr D:124 - Pro D:125	[ RasMol ]
		Val A:27 - Ala A:28	[ RasMol ]
		Val B:27 - Ala B:28	[ RasMol ]
		Val C:250 - Ser C:251	[ RasMol ]
		Val C:259 - Val C:260	[ RasMol ]
		Val C:27 - Ala C:28	[ RasMol ]
		Val C:73 - Gly C:74	[ RasMol ]
		Val D:27 - Ala D:28	[ RasMol ]

Biological Units
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	4e5y
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	FCL_HUMAN \| Q13630	:	4b8w 4b8z 4bkp 4bl5

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Description

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Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (38, 38)

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