4B8Z

Crystal structure of human GDP-L-fucose synthase with bound NADP and GDP, rhombohedral crystal form

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003824	molecular_function	catalytic activity
A	0005515	molecular_function	protein binding
A	0005829	cellular_component	cytosol
A	0007159	biological_process	leukocyte cell-cell adhesion
A	0009055	molecular_function	electron transfer activity
A	0009226	biological_process	nucleotide-sugar biosynthetic process
A	0010595	biological_process	positive regulation of endothelial cell migration
A	0016491	molecular_function	oxidoreductase activity
A	0016853	molecular_function	isomerase activity
A	0019673	biological_process	GDP-mannose metabolic process
A	0042351	biological_process	'de novo' GDP-L-fucose biosynthetic process
A	0042356	molecular_function	GDP-4-dehydro-D-rhamnose reductase activity
A	0042802	molecular_function	identical protein binding
A	0047918	molecular_function	GDP-mannose 3,5-epimerase activity
A	0050577	molecular_function	GDP-L-fucose synthase activity
A	0070062	cellular_component	extracellular exosome
A	1904906	biological_process	positive regulation of endothelial cell-matrix adhesion
B	0003824	molecular_function	catalytic activity
B	0005515	molecular_function	protein binding
B	0005829	cellular_component	cytosol
B	0007159	biological_process	leukocyte cell-cell adhesion
B	0009055	molecular_function	electron transfer activity
B	0009226	biological_process	nucleotide-sugar biosynthetic process
B	0010595	biological_process	positive regulation of endothelial cell migration
B	0016491	molecular_function	oxidoreductase activity
B	0016853	molecular_function	isomerase activity
B	0019673	biological_process	GDP-mannose metabolic process
B	0042351	biological_process	'de novo' GDP-L-fucose biosynthetic process
B	0042356	molecular_function	GDP-4-dehydro-D-rhamnose reductase activity
B	0042802	molecular_function	identical protein binding
B	0047918	molecular_function	GDP-mannose 3,5-epimerase activity
B	0050577	molecular_function	GDP-L-fucose synthase activity
B	0070062	cellular_component	extracellular exosome
B	1904906	biological_process	positive regulation of endothelial cell-matrix adhesion
C	0003824	molecular_function	catalytic activity
C	0005515	molecular_function	protein binding
C	0005829	cellular_component	cytosol
C	0007159	biological_process	leukocyte cell-cell adhesion
C	0009055	molecular_function	electron transfer activity
C	0009226	biological_process	nucleotide-sugar biosynthetic process
C	0010595	biological_process	positive regulation of endothelial cell migration
C	0016491	molecular_function	oxidoreductase activity
C	0016853	molecular_function	isomerase activity
C	0019673	biological_process	GDP-mannose metabolic process
C	0042351	biological_process	'de novo' GDP-L-fucose biosynthetic process
C	0042356	molecular_function	GDP-4-dehydro-D-rhamnose reductase activity
C	0042802	molecular_function	identical protein binding
C	0047918	molecular_function	GDP-mannose 3,5-epimerase activity
C	0050577	molecular_function	GDP-L-fucose synthase activity
C	0070062	cellular_component	extracellular exosome
C	1904906	biological_process	positive regulation of endothelial cell-matrix adhesion
D	0003824	molecular_function	catalytic activity
D	0005515	molecular_function	protein binding
D	0005829	cellular_component	cytosol
D	0007159	biological_process	leukocyte cell-cell adhesion
D	0009055	molecular_function	electron transfer activity
D	0009226	biological_process	nucleotide-sugar biosynthetic process
D	0010595	biological_process	positive regulation of endothelial cell migration
D	0016491	molecular_function	oxidoreductase activity
D	0016853	molecular_function	isomerase activity
D	0019673	biological_process	GDP-mannose metabolic process
D	0042351	biological_process	'de novo' GDP-L-fucose biosynthetic process
D	0042356	molecular_function	GDP-4-dehydro-D-rhamnose reductase activity
D	0042802	molecular_function	identical protein binding
D	0047918	molecular_function	GDP-mannose 3,5-epimerase activity
D	0050577	molecular_function	GDP-L-fucose synthase activity
D	0070062	cellular_component	extracellular exosome
D	1904906	biological_process	positive regulation of endothelial cell-matrix adhesion

Functional Information from PDB Data

site_id	AC1
Number of Residues	23
Details	BINDING SITE FOR RESIDUE NAP A 900

Chain	Residue
A	GLY14
A	LEU48
A	LEU69
A	ALA71
A	VAL73
A	MET93
A	CYS112
A	LEU113
A	SER114
A	TYR143
A	LYS147
A	SER16
A	PRO170
A	THR171
A	ASN172
A	VAL173
A	GLY17
A	LEU18
A	VAL19
A	SER42
A	SER43
A	ALA46
A	ASP47

---

site_id	AC2
Number of Residues	17
Details	BINDING SITE FOR RESIDUE GDP A 901

Chain	Residue
A	GLY75
A	LEU76
A	ASN172
A	GLY185
A	HIS186
A	VAL187
A	GLY190
A	LYS194
A	TRP208
A	GLY209
A	PRO213
A	ARG215
A	ILE252
A	SER276
A	ASP277
A	LYS282
A	HOH2003

---

site_id	AC3
Number of Residues	26
Details	BINDING SITE FOR RESIDUE NAP B 900

Chain	Residue
B	GLY14
B	SER16
B	GLY17
B	LEU18
B	VAL19
B	SER42
B	SER43
B	ALA46
B	ASP47
B	LEU48
B	LEU69
B	ALA70
B	ALA71
B	VAL73
B	MET93
B	CYS112
B	LEU113
B	SER114
B	TYR143
B	LYS147
B	PRO170
B	THR171
B	VAL173
B	HIS186
B	ARG320
B	HOH2001

---

site_id	AC4
Number of Residues	16
Details	BINDING SITE FOR RESIDUE GDP B 901

Chain	Residue
B	GLY75
B	LEU76
B	PHE77
B	ASN172
B	GLY185
B	HIS186
B	VAL187
B	LYS194
B	TRP208
B	GLY209
B	PRO213
B	ARG215
B	ILE252
B	SER276
B	ASP277
B	LYS282

---

site_id	AC5
Number of Residues	26
Details	BINDING SITE FOR RESIDUE NAP C 900

Chain	Residue
C	SER114
C	TYR143
C	LYS147
C	PRO170
C	THR171
C	VAL173
C	HIS186
C	ARG320
C	HOH2001
C	GLY14
C	SER16
C	GLY17
C	LEU18
C	VAL19
C	SER42
C	SER43
C	ALA46
C	ASP47
C	LEU48
C	LEU69
C	ALA70
C	ALA71
C	VAL73
C	MET93
C	CYS112
C	LEU113

---

site_id	AC6
Number of Residues	15
Details	BINDING SITE FOR RESIDUE GDP C 901

Chain	Residue
C	GLY75
C	LEU76
C	PHE77
C	ASN172
C	GLY185
C	HIS186
C	VAL187
C	LYS194
C	TRP208
C	GLY209
C	PRO213
C	ARG215
C	SER276
C	ASP277
C	LYS282

---

site_id	AC7
Number of Residues	26
Details	BINDING SITE FOR RESIDUE NAP D 900

Chain	Residue
D	GLY14
D	SER16
D	GLY17
D	LEU18
D	VAL19
D	SER42
D	SER43
D	ALA46
D	ASP47
D	LEU48
D	LEU69
D	ALA70
D	ALA71
D	VAL73
D	MET93
D	CYS112
D	LEU113
D	SER114
D	TYR143
D	LYS147
D	PRO170
D	THR171
D	ASN172
D	VAL173
D	HIS186
D	ARG320

---

site_id	AC8
Number of Residues	14
Details	BINDING SITE FOR RESIDUE GDP D 901

Chain	Residue
D	GLY75
D	LEU76
D	PHE77
D	ASN172
D	GLY185
D	HIS186
D	VAL187
D	LYS194
D	TRP208
D	PRO213
D	ARG215
D	SER276
D	ASP277
D	LYS282

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	Active site: {"description":"Proton donor/acceptor","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	40
Details	Binding site: {"evidences":[{"source":"PubMed","id":"23774504","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"APR-2013","submissionDatabase":"PDB data bank","title":"Crystal structure of human GDP-L-fucose synthase with bound NADP.","authoringGroup":["Structural genomics consortium (SGC)"]}}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"APR-2013","submissionDatabase":"PDB data bank","title":"Crystal structure of human GDP-L-fucose synthase with bound NADP.","authoringGroup":["Structural genomics consortium (SGC)"]}}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	16
Details	Binding site: {"evidences":[{"source":"Reference","evidenceCode":"ECO:0000305","citation":{"citationType":"submission","publicationDate":"APR-2013","submissionDatabase":"PDB data bank","title":"Crystal structure of human GDP-L-fucose synthase with bound NADP.","authoringGroup":["Structural genomics consortium (SGC)"]}}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	8
Details	Site: {"description":"Important for catalytic activity","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	4
Details	Site: {"description":"Lowers pKa of active site Tyr","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---