6ED7 | pdb_00006ed7

Crystal structure of 7,8-diaminopelargonic acid synthase bound to inhibitor MAC13772

PDB DOI: https://doi.org/10.2210/pdb6ED7/pdb

Classification: TRANSFERASE/ANTIBIOTIC
Organism(s): Escherichia coli
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-08-08 Released: 2019-08-21
Deposition Author(s): Brown, C.M., Zlitni, S., Chan, J., Brown, E.D., Junop, M.S.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.43 Å
R-Value Free:
0.237 (Depositor), 0.237 (DCC)
R-Value Work:
0.177 (Depositor), 0.177 (DCC)
R-Value Observed:
0.180 (Depositor)

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 7,8-diaminopelargonic acid synthase bound to inhibitor MAC13772

Brown, C.M., Zlitni, S., Chan, J., Brown, E.D., Junop, M.S.

To be published.

Macromolecule Content

Total Structure Weight: 384.2 kDa
Atom Count: 27,268
Modeled Residue Count: 3,432
Deposited Residue Count: 3,432
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
7,8-diamino-pelargonic acid aminotransferase	A, B, C, D, E A, B, C, D, E, F, G, H	429	Escherichia coli	Mutation(s): 0 Gene Names: bioA, EL75_3021, EL79_3111, EL80_3072 EC: 2.6.1.62
UniProt
Find proteins for P12995 (Escherichia coli (strain K12)) Explore P12995 Go to UniProtKB: P12995
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P12995
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PLP Query on PLP Download:Ideal Coordinates CCD File SDF format, chain DA [auth H] SDF format, chain I [auth A] SDF format, chain X [auth F] SDF format, chain U [auth E] SDF format, chain R [auth D] SDF format, chain O [auth C] SDF format, chain L [auth B] SDF format, chain BA [auth G] MOL2 format, chain DA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain X [auth F] MOL2 format, chain U [auth E] MOL2 format, chain R [auth D] MOL2 format, chain O [auth C] MOL2 format, chain L [auth B] MOL2 format, chain BA [auth G] mmCIF format, chain DA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain X [auth F] mmCIF format, chain U [auth E] mmCIF format, chain R [auth D] mmCIF format, chain O [auth C] mmCIF format, chain L [auth B] mmCIF format, chain BA [auth G]	BA [auth G] DA [auth H] I [auth A] L [auth B] O [auth C] BA [auth G], DA [auth H], I [auth A], L [auth B], O [auth C], R [auth D], U [auth E], X [auth F]	PYRIDOXAL-5'-PHOSPHATE C₈ H₁₀ N O₆ P NGVDGCNFYWLIFO-UHFFFAOYSA-N		Interactions Focus chain BA [auth G] Focus chain DA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F] Interactions & Density Focus chain BA [auth G] Focus chain DA [auth H] Focus chain I [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain R [auth D] Focus chain U [auth E] Focus chain X [auth F]
J4J Query on J4J Download:Ideal Coordinates CCD File SDF format, chain FA [auth H] SDF format, chain N [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain V [auth E] SDF format, chain Z [auth F] SDF format, chain Y [auth F] SDF format, chain W [auth E] SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain M [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain EA [auth H] SDF format, chain CA [auth G] SDF format, chain AA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain N [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain V [auth E] MOL2 format, chain Z [auth F] MOL2 format, chain Y [auth F] MOL2 format, chain W [auth E] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain EA [auth H] MOL2 format, chain CA [auth G] MOL2 format, chain AA [auth G] mmCIF format, chain FA [auth H] mmCIF format, chain N [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain V [auth E] mmCIF format, chain Z [auth F] mmCIF format, chain Y [auth F] mmCIF format, chain W [auth E] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain EA [auth H] mmCIF format, chain CA [auth G] mmCIF format, chain AA [auth G]	AA [auth G] CA [auth G] EA [auth H] FA [auth H] J [auth A] AA [auth G], CA [auth G], EA [auth H], FA [auth H], J [auth A], K [auth A], M [auth B], N [auth B], P [auth C], Q [auth C], S [auth D], T [auth D], V [auth E], W [auth E], Y [auth F], Z [auth F]	2-[(2-nitrophenyl)sulfanyl]acetohydrazide C₈ H₉ N₃ O₃ S CZXFCCXLFQCYBK-UHFFFAOYSA-N		Interactions Focus chain AA [auth G] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain FA [auth H] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain V [auth E] Focus chain W [auth E] Focus chain Y [auth F] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth G] Focus chain CA [auth G] Focus chain EA [auth H] Focus chain FA [auth H] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Focus chain T [auth D] Focus chain V [auth E] Focus chain W [auth E] Focus chain Y [auth F] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.43 Å
R-Value Free: 0.237 (Depositor), 0.237 (DCC)
R-Value Work: 0.177 (Depositor), 0.177 (DCC)
R-Value Observed: 0.180 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 122.43	α = 90
b = 111.57	β = 92.08
c = 136.12	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-08-21

Deposition Author(s):

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	--

Revision History (Full details and data files)

Version 1.0: 2019-08-21
Type: Initial release
Version 1.1: 2020-01-08
Changes: Author supporting evidence
Version 1.2: 2025-04-02
Changes: Data collection, Database references, Structure summary