4BL5

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

PDB DOI: https://doi.org/10.2210/pdb4BL5/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-05-01 Released: 2014-05-21
Deposition Author(s): 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.

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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.

Macromolecule Content

Total Structure Weight: 469.75 kDa
Atom Count: 29,916
Modelled Residue Count: 3,805
Deposited Residue Count: 4,032
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GDP-L-FUCOSE SYNTHASE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	336	Homo sapiens	Mutation(s): 0 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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13630
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain BA [auth H] SDF format, chain DA [auth I] SDF format, chain FA [auth J] SDF format, chain HA [auth K] SDF format, chain JA [auth L] SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain S [auth D] SDF format, chain U [auth E] SDF format, chain W [auth F] SDF format, chain Z [auth G] MOL2 format, chain BA [auth H] MOL2 format, chain DA [auth I] MOL2 format, chain FA [auth J] MOL2 format, chain HA [auth K] MOL2 format, chain JA [auth L] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] MOL2 format, chain U [auth E] MOL2 format, chain W [auth F] MOL2 format, chain Z [auth G] mmCIF format, chain BA [auth H] mmCIF format, chain DA [auth I] mmCIF format, chain FA [auth J] mmCIF format, chain HA [auth K] mmCIF format, chain JA [auth L] mmCIF format, chain M [auth A] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth D] mmCIF format, chain U [auth E] mmCIF format, chain W [auth F] mmCIF format, chain Z [auth G]	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		Interactions Focus chain BA [auth H] Focus chain DA [auth I] Focus chain FA [auth J] Focus chain HA [auth K] Focus chain JA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Z [auth G] Interactions & Density Focus chain BA [auth H] Focus chain DA [auth I] Focus chain FA [auth J] Focus chain HA [auth K] Focus chain JA [auth L] Focus chain M [auth A] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Z [auth G]
GFB Query on GFB Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain EA [auth I] SDF format, chain GA [auth J] SDF format, chain IA [auth K] SDF format, chain KA [auth L] SDF format, chain N [auth A] SDF format, chain P [auth B] SDF format, chain R [auth C] SDF format, chain T [auth D] SDF format, chain V [auth E] SDF format, chain X [auth F] SDF format, chain CA [auth H] MOL2 format, chain AA [auth G] MOL2 format, chain EA [auth I] MOL2 format, chain GA [auth J] MOL2 format, chain IA [auth K] MOL2 format, chain KA [auth L] MOL2 format, chain N [auth A] MOL2 format, chain P [auth B] MOL2 format, chain R [auth C] MOL2 format, chain T [auth D] MOL2 format, chain V [auth E] MOL2 format, chain X [auth F] MOL2 format, chain CA [auth H] mmCIF format, chain AA [auth G] mmCIF format, chain EA [auth I] mmCIF format, chain GA [auth J] mmCIF format, chain IA [auth K] mmCIF format, chain KA [auth L] mmCIF format, chain N [auth A] mmCIF format, chain P [auth B] mmCIF format, chain R [auth C] mmCIF format, chain T [auth D] mmCIF format, chain V [auth E] mmCIF format, chain X [auth F] mmCIF format, chain CA [auth H]	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		Interactions Focus chain AA [auth G] Focus chain CA [auth H] Focus chain EA [auth I] Focus chain GA [auth J] Focus chain IA [auth K] Focus chain KA [auth L] Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F] Interactions & Density Focus chain AA [auth G] Focus chain CA [auth H] Focus chain EA [auth I] Focus chain GA [auth J] Focus chain IA [auth K] Focus chain KA [auth L] Focus chain N [auth A] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain V [auth E] Focus chain X [auth F]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain Y [auth F] MOL2 format, chain Y [auth F] mmCIF format, chain Y [auth F]	Y [auth F]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain Y [auth F] Interactions & Density Focus chain Y [auth F]

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 = 90.407	α = 72.54
b = 90.478	β = 72.64
c = 147.518	γ = 60.14

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-05-21

Deposition Author(s):

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
Version 1.2: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description