1CDE

STRUCTURES OF APO AND COMPLEXED ESCHERICHIA COLI GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE

PDB DOI: https://doi.org/10.2210/pdb1CDE/pdb

Classification: TRANSFERASE(FORMYL)
Organism(s): Escherichia coli
Mutation(s): No

Deposited: 1992-05-15 Released: 1993-10-31
Deposition Author(s): Almassy, R.J., Janson, C.A., Kan, C.-C., Hostomska, Z.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 ?
R-Value Work: 0.250
R-Value Observed: 0.250

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structures of apo and complexed Escherichia coli glycinamide ribonucleotide transformylase.

Almassy, R.J., Janson, C.A., Kan, C.C., Hostomska, Z.

(1992) Proc Natl Acad Sci U S A 89: 6114-6118

PubMed: 1631098 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1073/pnas.89.13.6114
Primary Citation of Related Structures:
1CDD, 1CDE

PubMed Abstract:
The three-dimensional structure of phosphoribosylglycinamide formyltransferase (10-formyltetrahydrofolate:5'-phosphoribosylglycinamide formyltransferase, EC 2.1.2.2) has been solved both as an apoenzyme at 2.8-A resolution and as a ternary complex with the substrate glycinamide ribonucleotide and a folate inhibitor at 2.5-A resolution. The structure is a modified doubly wound alpha/beta sheet with flexibility in the active site, including a disordered loop in the apo structure, which is ordered in the ternary complex structure. This enzyme is a target for anti-cancer therapy and now for structure-based drug design.

Organizational Affiliation

Agouron Pharmaceuticals, San Diego, CA 92121.

Macromolecule Content

Total Structure Weight: 95.96 kDa
Atom Count: 6,668
Modelled Residue Count: 836
Deposited Residue Count: 848
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHOSPHORIBOSYL-GLYCINAMIDE FORMYLTRANSFERASE	A, B, C, D	212	Escherichia coli	Mutation(s): 0 EC: 2.1.2.2
UniProt
Find proteins for P08179 (Escherichia coli (strain K12)) Explore P08179 Go to UniProtKB: P08179
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08179
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DZF Query on DZF Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth C] SDF format, chain L [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth C] MOL2 format, chain L [auth D] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth C] mmCIF format, chain L [auth D]	F [auth A], H [auth B], J [auth C], L [auth D]	5-DEAZAFOLIC ACID C₂₀ H₂₀ N₆ O₆ NFARHPAOOHOWAL-AWEZNQCLSA-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]
GAR Query on GAR 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]	GLYCINAMIDE RIBONUCLEOTIDE C₇ H₁₃ N₂ O₈ P OBQMLSFOUZUIOB-SHUUEZRQSA-L		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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 ?
R-Value Work: 0.250
R-Value Observed: 0.250
Space Group: P 1

Unit Cell:

Length ( ? )	Angle ( ? )
a = 76.7	α = 111.5
b = 72.6	β = 82.8
c = 57	γ = 62.6

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 1993-10-31

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 1993-10-31
Type: Initial release
Version 1.1: 2008-03-24
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2024-02-07
Changes: Data collection, Database references, Derived calculations, Other

Prepare Data

Validate Data

Deposit Data

Help and Resources

1CDE

STRUCTURES OF APO AND COMPLEXED ESCHERICHIA COLI GLYCINAMIDE RIBONUCLEOTIDE TRANSFORMYLASE

Structures of apo and complexed Escherichia coli glycinamide ribonucleotide transformylase.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)