4BL5

Crystal structure of human GDP-L-fucose synthase with bound NADP and product GDP-L-fucose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Crystal Structure of Human Gdp-L-Fucose Synthase with Bound Nadp and Product Gdp-L-Fucose

Vollmar, M.Shafqat, N.Rojkova, A.Krojer, T.Bradley, A.Raynor, J.W.Kavanagh, K.von Delft, F.Arrowsmith, C.H.Bountra, C.Edwards, A.Oppermann, U.Yue, W.W.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GDP-L-FUCOSE SYNTHASE
A, B, C, D, E, F, G, H, I, J, K, L
A, B, C, D, E, F, G, H, I, J, K, L
336Homo sapiensMutation(s): 0 
Gene Names: GFUSSDR4E1TSTA3
EC: 1.1.1.271
UniProt & NIH Common Fund Data Resources
Find proteins for Q13630 (Homo sapiens)
Explore Q13630 
Go to UniProtKB:  Q13630
PHAROS:  Q13630
GTEx:  ENSG00000104522 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13630
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAP
Query on NAP

Download Ideal Coordinates CCD File 
BA [auth H],
DA [auth I],
FA [auth J],
HA [auth K],
JA [auth L],
BA [auth H],
DA [auth I],
FA [auth J],
HA [auth K],
JA [auth L],
M [auth A],
O [auth B],
Q [auth C],
S [auth D],
U [auth E],
W [auth F],
Z [auth G]
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
C21 H28 N7 O17 P3
XJLXINKUBYWONI-NNYOXOHSSA-N
 Ligand Interaction
GFB
Query on GFB

Download Ideal Coordinates CCD File 
AA [auth G],
CA [auth H],
EA [auth I],
GA [auth J],
IA [auth K],
AA [auth G],
CA [auth H],
EA [auth I],
GA [auth J],
IA [auth K],
KA [auth L],
N [auth A],
P [auth B],
R [auth C],
T [auth D],
V [auth E],
X [auth F]
GUANOSINE-5'-DIPHOSPHATE-BETA-L-FUCOPYRANOSE
C16 H25 N5 O15 P2
LQEBEXMHBLQMDB-JGQUBWHWSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
Y [auth F]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.222 
  • R-Value Observed: 0.225 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.407α = 72.54
b = 90.478β = 72.64
c = 147.518γ = 60.14
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-05-21
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Database references