7CVH | pdb_00007cvh

Human Fructose-1,6-bisphosphatase 1 in complex with geranylgeranyl diphosphate

PDB DOI: https://doi.org/10.2210/pdb7CVH/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-08-26 Released: 2021-09-08
Deposition Author(s): Chen, Y., Zhang, J., Li, C., Cao, Y.
Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free:
0.218 (Depositor), 0.220 (DCC)
R-Value Work:
0.178 (Depositor), 0.180 (DCC)
R-Value Observed:
0.179 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

The structural basis for GGPP activation on the enzymatic activities FBP1

Chen, Y., Zhang, J., Li, C., Cao, Y.

To be published.

Macromolecule Content

Total Structure Weight: 150.94 kDa
Atom Count: 11,079
Modeled Residue Count: 1,278
Deposited Residue Count: 1,352
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fructose-1,6-bisphosphatase 1	A, B [auth C], C [auth B], D	338	Homo sapiens	Mutation(s): 0 Gene Names: FBP1, FBP EC: 3.1.3.11
UniProt & NIH Common Fund Data Resources
Find proteins for P09467 (Homo sapiens) Explore P09467 Go to UniProtKB: P09467
PHAROS: P09467 GTEx: ENSG00000165140
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P09467
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GRG (Subject of Investigation/LOI) Query on GRG Download Ideal Coordinates CCD File SDF format, chain Q [auth D] MOL2 format, chain Q [auth D] mmCIF format, chain Q [auth D]	Q [auth D]	GERANYLGERANYL DIPHOSPHATE C₂₀ H₃₆ O₇ P₂ OINNEUNVOZHBOX-QIRCYJPOSA-N		Interactions Focus chain Q [auth D] Interactions & Density Focus chain Q [auth D]
AMP Query on AMP Download Ideal Coordinates CCD File SDF format, chain L [auth C] SDF format, chain P [auth B] SDF format, chain U [auth D] SDF format, chain H [auth A] MOL2 format, chain L [auth C] MOL2 format, chain P [auth B] MOL2 format, chain U [auth D] MOL2 format, chain H [auth A] mmCIF format, chain L [auth C] mmCIF format, chain P [auth B] mmCIF format, chain U [auth D] mmCIF format, chain H [auth A]	H [auth A], L [auth C], P [auth B], U [auth D]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain H [auth A] Focus chain L [auth C] Focus chain P [auth B] Focus chain U [auth D] Interactions & Density Focus chain H [auth A] Focus chain L [auth C] Focus chain P [auth B] Focus chain U [auth D]
FBP Query on FBP Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain R [auth D] SDF format, chain M [auth B] SDF format, chain I [auth C] MOL2 format, chain E [auth A] MOL2 format, chain R [auth D] MOL2 format, chain M [auth B] MOL2 format, chain I [auth C] mmCIF format, chain E [auth A] mmCIF format, chain R [auth D] mmCIF format, chain M [auth B] mmCIF format, chain I [auth C]	E [auth A], I [auth C], M [auth B], R [auth D]	1,6-di-O-phosphono-beta-D-fructofuranose C₆ H₁₄ O₁₂ P₂ RNBGYGVWRKECFJ-ARQDHWQXSA-N		Interactions Focus chain E [auth A] Focus chain I [auth C] Focus chain M [auth B] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth C] Focus chain M [auth B] Focus chain R [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain K [auth C] SDF format, chain J [auth C] SDF format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain K [auth C] MOL2 format, chain J [auth C] MOL2 format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain K [auth C] mmCIF format, chain J [auth C] mmCIF format, chain G [auth A]	F [auth A] G [auth A] J [auth C] K [auth C] N [auth B] F [auth A], G [auth A], J [auth C], K [auth C], N [auth B], O [auth B], S [auth D], T [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth C] Focus chain K [auth C] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth C] Focus chain K [auth C] Focus chain N [auth B] Focus chain O [auth B] Focus chain S [auth D] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.09 Å
R-Value Free: 0.218 (Depositor), 0.220 (DCC)
R-Value Work: 0.178 (Depositor), 0.180 (DCC)
R-Value Observed: 0.179 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.392	α = 90
b = 83.426	β = 90
c = 277.355	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2021-09-08

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2018YFC1004704
Ministry of Science and Technology (MoST, China)	China	2018YFC1004703
National Natural Science Foundation of China (NSFC)	China	31670849
National Natural Science Foundation of China (NSFC)	China	U1632132