Structure of PDB 5in4 Chain C

Receptor sequence

>5in4C (length=351) Species: 9606 (Homo sapiens) [Search protein sequence]

GRNVALITGITGQDGSYLAEFLLEKGYEVHGIVRRSSSFNTGRIEHLYKN
PQAHIEGNMKLHYGDLTDSTCLVKIINEVKPTEIYNLGAQSHVKISFDLA
EYTADVDGVGTLRLLDAVKTCGLINSVKFYQASTSELYGKVQEIPQKETT
PFYPRSPYGAAKLYAYWIVVNFREAYNLFAVNGILFNHESPRRGANFVTR
KISRSVAKIYLGQLECFSLGNLDAKRDWGHAKDYVEAMWLMLQNDEPEDF
VIATGEVHSVREFVEKSFLHIGKTIVWEGKNENEVGRCKETGKVHVTVDL
KYYRPTEVDFLQGDCTKAKQKLNWKPRVAFDELVREMVHADVELMRTNPN
A

3D structure

PDB

5in4 Facile Modulation of Antibody Fucosylation with Small Molecule Fucostatin Inhibitors and Cocrystal Structure with GDP-Mannose 4,6-Dehydratase.

Chain

Resolution

1.6 Å

3D
structure

Catalytic site residues are labeled in the structure
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Enzymatic activity

Catalytic site (original residue number in PDB)	T155 S156 E157 Y179 K183
Catalytic site (residue number reindexed from 1)	T134 S135 E136 Y158 K162
Enzyme Commision number	4.2.1.47: GDP-mannose 4,6-dehydratase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	NAP	C	G30 T32 G33 Q34 D35 R55 D86 L87 L108 G109 A110 S112 V127 A153 S154 T155 Y179 K183 L206 N208 H209 R214	G9 T11 G12 Q13 D14 R34 D65 L66 L87 G88 A89 S91 V106 A132 S133 T134 Y158 K162 L185 N187 H188 R193
BS02	GDP	C	E157 N208 F218 V219 K222 L240 G241 N242 R247 R325 E328	E136 N187 F197 V198 K201 L219 G220 N221 R226 R304 E307
BS03	6CK	C	F60 T62 Y69 H75 E77 L82 Y84	F39 T41 Y48 H54 E56 L61 Y63	MOAD: Kd=11uM
BS04	6CK	C	A216 N217 K222 R225 Y323	A195 N196 K201 R204 Y302	MOAD: Kd=11uM
BS05	NAP	C	R56 S57 S58	R35 S36 S37

Gene Ontology

	Molecular Function
GO:0005515	protein binding
GO:0008446	GDP-mannose 4,6-dehydratase activity
GO:0016829	lyase activity
GO:0042802	identical protein binding
GO:0070401	NADP+ binding

	Biological Process
GO:0007219	Notch signaling pathway
GO:0019673	GDP-mannose metabolic process
GO:0042350	GDP-L-fucose biosynthetic process
GO:0042351	'de novo' GDP-L-fucose biosynthetic process

	Cellular Component
GO:0005737	cytoplasm
GO:0005829	cytosol
GO:0070062	extracellular exosome

View graph for
Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:5in4, PDBe:5in4, PDBj:5in4
PDBsum	5in4
PubMed	27434622
UniProt	O60547\|GMDS_HUMAN GDP-mannose 4,6 dehydratase (Gene Name=GMDS)

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