6Q94

Crystal structure of human GDP-D-mannose 4,6-dehydratase (S156D) in complex with GDP-Man

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005515	molecular_function	protein binding
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0007219	biological_process	Notch signaling pathway
A	0008446	molecular_function	GDP-mannose 4,6-dehydratase activity
A	0016829	molecular_function	lyase activity
A	0019673	biological_process	GDP-mannose metabolic process
A	0042350	biological_process	GDP-L-fucose biosynthetic process
A	0042351	biological_process	'de novo' GDP-L-fucose biosynthetic process
A	0042802	molecular_function	identical protein binding
A	0070062	cellular_component	extracellular exosome
A	0070401	molecular_function	NADP+ binding
B	0005515	molecular_function	protein binding
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0007219	biological_process	Notch signaling pathway
B	0008446	molecular_function	GDP-mannose 4,6-dehydratase activity
B	0016829	molecular_function	lyase activity
B	0019673	biological_process	GDP-mannose metabolic process
B	0042350	biological_process	GDP-L-fucose biosynthetic process
B	0042351	biological_process	'de novo' GDP-L-fucose biosynthetic process
B	0042802	molecular_function	identical protein binding
B	0070062	cellular_component	extracellular exosome
B	0070401	molecular_function	NADP+ binding
C	0005515	molecular_function	protein binding
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0007219	biological_process	Notch signaling pathway
C	0008446	molecular_function	GDP-mannose 4,6-dehydratase activity
C	0016829	molecular_function	lyase activity
C	0019673	biological_process	GDP-mannose metabolic process
C	0042350	biological_process	GDP-L-fucose biosynthetic process
C	0042351	biological_process	'de novo' GDP-L-fucose biosynthetic process
C	0042802	molecular_function	identical protein binding
C	0070062	cellular_component	extracellular exosome
C	0070401	molecular_function	NADP+ binding
D	0005515	molecular_function	protein binding
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0007219	biological_process	Notch signaling pathway
D	0008446	molecular_function	GDP-mannose 4,6-dehydratase activity
D	0016829	molecular_function	lyase activity
D	0019673	biological_process	GDP-mannose metabolic process
D	0042350	biological_process	GDP-L-fucose biosynthetic process
D	0042351	biological_process	'de novo' GDP-L-fucose biosynthetic process
D	0042802	molecular_function	identical protein binding
D	0070062	cellular_component	extracellular exosome
D	0070401	molecular_function	NADP+ binding
E	0005515	molecular_function	protein binding
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0007219	biological_process	Notch signaling pathway
E	0008446	molecular_function	GDP-mannose 4,6-dehydratase activity
E	0016829	molecular_function	lyase activity
E	0019673	biological_process	GDP-mannose metabolic process
E	0042350	biological_process	GDP-L-fucose biosynthetic process
E	0042351	biological_process	'de novo' GDP-L-fucose biosynthetic process
E	0042802	molecular_function	identical protein binding
E	0070062	cellular_component	extracellular exosome
E	0070401	molecular_function	NADP+ binding
F	0005515	molecular_function	protein binding
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0007219	biological_process	Notch signaling pathway
F	0008446	molecular_function	GDP-mannose 4,6-dehydratase activity
F	0016829	molecular_function	lyase activity
F	0019673	biological_process	GDP-mannose metabolic process
F	0042350	biological_process	GDP-L-fucose biosynthetic process
F	0042351	biological_process	'de novo' GDP-L-fucose biosynthetic process
F	0042802	molecular_function	identical protein binding
F	0070062	cellular_component	extracellular exosome
F	0070401	molecular_function	NADP+ binding
G	0005515	molecular_function	protein binding
G	0005737	cellular_component	cytoplasm
G	0005829	cellular_component	cytosol
G	0007219	biological_process	Notch signaling pathway
G	0008446	molecular_function	GDP-mannose 4,6-dehydratase activity
G	0016829	molecular_function	lyase activity
G	0019673	biological_process	GDP-mannose metabolic process
G	0042350	biological_process	GDP-L-fucose biosynthetic process
G	0042351	biological_process	'de novo' GDP-L-fucose biosynthetic process
G	0042802	molecular_function	identical protein binding
G	0070062	cellular_component	extracellular exosome
G	0070401	molecular_function	NADP+ binding
H	0005515	molecular_function	protein binding
H	0005737	cellular_component	cytoplasm
H	0005829	cellular_component	cytosol
H	0007219	biological_process	Notch signaling pathway
H	0008446	molecular_function	GDP-mannose 4,6-dehydratase activity
H	0016829	molecular_function	lyase activity
H	0019673	biological_process	GDP-mannose metabolic process
H	0042350	biological_process	GDP-L-fucose biosynthetic process
H	0042351	biological_process	'de novo' GDP-L-fucose biosynthetic process
H	0042802	molecular_function	identical protein binding
H	0070062	cellular_component	extracellular exosome
H	0070401	molecular_function	NADP+ binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	22
Details	binding site for residue NAP B 401

Chain	Residue
A	ARG56
B	ASN61
B	ASP86
B	LEU87
B	LEU108
B	GLY109
B	ALA110
B	SER112
B	TYR123
B	ALA153
B	TYR179
A	SER57
B	LYS183
B	ARG214
B	GDD402
A	SER58
B	GLY30
B	THR32
B	GLY33
B	GLN34
B	ASP35
B	ARG55

---

site_id	AC2
Number of Residues	20
Details	binding site for residue GDD B 402

Chain	Residue
B	SER112
B	HIS113
B	VAL114
B	THR155
B	TYR179
B	ASN208
B	ARG214
B	ASN217
B	PHE218
B	VAL219
B	LYS222
B	LEU240
B	GLY241
B	ASN242
B	ALA245
B	ARG247
B	VAL281
B	ARG325
B	GLU328
B	NAP401

---

site_id	AC3
Number of Residues	22
Details	binding site for residue NAP A 401

Chain	Residue
A	GLY30
A	THR32
A	GLY33
A	GLN34
A	ASP35
A	ARG55
A	ASN61
A	ASP86
A	LEU87
A	LEU108
A	GLY109
A	ALA110
A	SER112
A	TYR123
A	VAL127
A	ALA153
A	TYR179
A	LYS183
A	GDD402
B	ARG56
B	SER57
B	SER58

---

site_id	AC4
Number of Residues	21
Details	binding site for residue GDD A 402

Chain	Residue
A	SER112
A	THR155
A	ASP156
A	GLU157
A	TYR179
A	PHE207
A	ASN208
A	ARG214
A	ASN217
A	PHE218
A	VAL219
A	LYS222
A	LEU240
A	GLY241
A	ASN242
A	ALA245
A	ARG247
A	TYR323
A	ARG325
A	GLU328
A	NAP401

---

site_id	AC5
Number of Residues	20
Details	binding site for residue NAP C 401

Chain	Residue
C	ALA153
C	TYR179
C	LYS183
C	GDD402
E	ARG56
E	SER58
C	GLY30
C	THR32
C	GLY33
C	GLN34
C	ASP35
C	ARG55
C	ASP86
C	LEU87
C	LEU108
C	GLY109
C	ALA110
C	SER112
C	TYR123
C	VAL127

---

site_id	AC6
Number of Residues	22
Details	binding site for residue GDD C 402

Chain	Residue
C	SER112
C	VAL114
C	THR155
C	ASP156
C	GLU157
C	TYR179
C	LEU206
C	PHE207
C	ASN208
C	ARG214
C	ASN217
C	PHE218
C	VAL219
C	LYS222
C	GLY241
C	ASN242
C	ALA245
C	ARG247
C	VAL281
C	ARG325
C	GLU328
C	NAP401

---

site_id	AC7
Number of Residues	23
Details	binding site for residue NAP D 401

Chain	Residue
D	GLY30
D	THR32
D	GLY33
D	GLN34
D	ASP35
D	ARG55
D	ASN61
D	ASP86
D	LEU87
D	LEU108
D	GLY109
D	ALA110
D	SER112
D	TYR123
D	ALA153
D	THR155
D	TYR179
D	LYS183
D	ARG214
D	GDD402
F	ARG56
F	SER57
F	SER58

---

site_id	AC8
Number of Residues	22
Details	binding site for residue GDD D 402

Chain	Residue
D	SER112
D	VAL114
D	THR155
D	ASP156
D	GLU157
D	TYR179
D	PHE207
D	ASN208
D	ARG214
D	ASN217
D	PHE218
D	VAL219
D	LYS222
D	LEU240
D	GLY241
D	ASN242
D	ALA245
D	ARG247
D	VAL281
D	ARG325
D	GLU328
D	NAP401

---

site_id	AC9
Number of Residues	3
Details	binding site for residue EDO D 403

Chain	Residue
D	TYR84
F	ASN217
F	TYR323

---

site_id	AD1
Number of Residues	1
Details	binding site for residue EDO D 404

Chain	Residue
D	ASN217

---

site_id	AD2
Number of Residues	21
Details	binding site for residue NAP E 401

Chain	Residue
C	ARG56
C	SER57
C	SER58
E	GLY30
E	THR32
E	GLY33
E	GLN34
E	ASP35
E	ARG55
E	ASP86
E	LEU87
E	LEU108
E	GLY109
E	ALA110
E	SER112
E	TYR123
E	VAL127
E	ALA153
E	TYR179
E	LYS183
E	GDD402

---

site_id	AD3
Number of Residues	21
Details	binding site for residue GDD E 402

Chain	Residue
E	SER112
E	VAL114
E	THR155
E	ASP156
E	TYR179
E	PHE207
E	ASN208
E	ARG214
E	ASN217
E	PHE218
E	VAL219
E	LYS222
E	LEU240
E	GLY241
E	ASN242
E	ALA245
E	ARG247
E	VAL281
E	ARG325
E	GLU328
E	NAP401

---

site_id	AD4
Number of Residues	21
Details	binding site for residue GDD F 401

Chain	Residue
F	SER112
F	VAL114
F	THR155
F	ASP156
F	TYR179
F	LEU206
F	PHE207
F	ASN208
F	ARG214
F	ASN217
F	PHE218
F	VAL219
F	LYS222
F	GLY241
F	ASN242
F	ALA245
F	ARG247
F	VAL281
F	ARG325
F	GLU328
F	NAP402

---

site_id	AD5
Number of Residues	22
Details	binding site for residue NAP F 402

Chain	Residue
D	ARG56
D	SER57
D	SER58
F	GLY30
F	THR32
F	GLY33
F	GLN34
F	ASP35
F	ARG55
F	ASN61
F	ASP86
F	LEU87
F	LEU108
F	GLY109
F	ALA110
F	SER112
F	TYR123
F	VAL127
F	ALA153
F	TYR179
F	LYS183
F	GDD401

---

site_id	AD6
Number of Residues	22
Details	binding site for residue NAP G 401

Chain	Residue
G	GLY30
G	THR32
G	GLY33
G	GLN34
G	ASP35
G	ARG55
G	ASN61
G	ASP86
G	LEU87
G	LEU108
G	GLY109
G	ALA110
G	SER112
G	TYR123
G	VAL127
G	ALA153
G	TYR179
G	LYS183
G	GDD402
H	ARG56
H	SER57
H	SER58

---

site_id	AD7
Number of Residues	21
Details	binding site for residue GDD G 402

Chain	Residue
G	SER112
G	HIS113
G	VAL114
G	THR155
G	ASP156
G	TYR179
G	PHE207
G	ASN208
G	ARG214
G	ASN217
G	PHE218
G	VAL219
G	LYS222
G	LEU240
G	GLY241
G	ASN242
G	ALA245
G	ARG247
G	ARG325
G	GLU328
G	NAP401

---

site_id	AD8
Number of Residues	2
Details	binding site for residue EDO G 403

Chain	Residue
G	PHE60
G	HIS75

---

site_id	AD9
Number of Residues	20
Details	binding site for residue NAP H 401

Chain	Residue
G	ARG56
G	SER58
H	GLY30
H	THR32
H	GLY33
H	GLN34
H	ASP35
H	ARG55
H	ASP86
H	LEU87
H	LEU108
H	GLY109
H	ALA110
H	SER112
H	TYR123
H	VAL127
H	THR155
H	TYR179
H	LYS183
H	GDD402

---

site_id	AE1
Number of Residues	20
Details	binding site for residue GDD H 402

Chain	Residue
H	SER112
H	VAL114
H	THR155
H	ASP156
H	TYR179
H	ASN208
H	ARG214
H	ASN217
H	PHE218
H	VAL219
H	LYS222
H	LEU240
H	GLY241
H	ASN242
H	ALA245
H	ARG247
H	TYR323
H	ARG325
H	GLU328
H	NAP401

---

site_id	AE2
Number of Residues	1
Details	binding site for residue EDO H 403

Chain	Residue
H	TYR323

---

Functional Information from PROSITE/UniProt

site_id	PS00061
Number of Residues	29
Details	ADH_SHORT Short-chain dehydrogenases/reductases family signature. PqkettpfypRspYGAAKLYAyWIVvNFR

Chain	Residue	Details
B	PRO166-ARG194

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	Active site: {"evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	16
Details	Active site: {"description":"Nucleophile","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	136
Details	Binding site: {"evidences":[{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"APR-2004","submissionDatabase":"PDB data bank","title":"Crystal structure and biophysical characterization of human GDP-D-mannose 4,6-dehydratase.","authors":["Vedadi M.","Walker J.R.","Sharma S.","Houston S.","Wasney G.","Loppnau P.","Oppermann U."]}}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	8
Details	Modified residue: {"description":"Phosphotyrosine","evidences":[{"source":"PubMed","id":"23186163","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---