4B8Z

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

PDB DOI: https://doi.org/10.2210/pdb4B8Z/pdb

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

Deposited: 2012-08-31 Released: 2013-02-06
Deposition Author(s): Vollmar, M., Krojer, T., Shafqat, N., Rojkova, A., Bunkoczi, G., Yue, W.W., Kavanagh, K., von Delft, F., Weigelt, J., Arrowsmith, C.H., Bountra, C., Edwards, A., Oppermann, U.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 ?
R-Value Free: 0.261
R-Value Work: 0.233
R-Value Observed: 0.235

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of Human Gdp-L-Fucose Synthase with Bound Nadp and Gdp, Rhombohedral Crystal Form

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

To be published.

Macromolecule Content

Total Structure Weight: 148.75 kDa
Atom Count: 9,492
Modelled Residue Count: 1,254
Deposited Residue Count: 1,280
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	320	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAP Query on NAP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] SDF format, chain I [auth C] SDF format, chain K [auth D] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] MOL2 format, chain I [auth C] MOL2 format, chain K [auth D] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B] mmCIF format, chain I [auth C] mmCIF format, chain K [auth D]	E [auth A], G [auth B], I [auth C], K [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C₂₁ H₂₈ N₇ O₁₇ P₃ XJLXINKUBYWONI-NNYOXOHSSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain I [auth C] Focus chain K [auth D]
GDP Query on GDP Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth C] SDF format, chain L [auth D] SDF format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] MOL2 format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D] mmCIF format, chain H [auth B]	F [auth A], H [auth B], J [auth C], L [auth D]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain L [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 ?
R-Value Free: 0.261
R-Value Work: 0.233
R-Value Observed: 0.235
Space Group: H 3

Unit Cell:

Length ( ? )	Angle ( ? )
a = 91.447	α = 90
b = 91.447	β = 90
c = 429.13	γ = 120

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-02-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-02-06
Type: Initial release
Version 1.1: 2018-01-24
Changes: Database references
Version 1.2: 2018-06-20
Changes: Data collection, Derived calculations
Version 1.3: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description

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4B8Z

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

Crystal Structure of Human Gdp-L-Fucose Synthase with Bound Nadp and Gdp, Rhombohedral Crystal Form

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)