4KQ6 | pdb_00004kq6

Product complex of lumazine synthase from candida glabrata

PDB DOI: https://doi.org/10.2210/pdb4KQ6/pdb
Entry: 4KQ6 supersedes: 4GEF

Classification: TRANSFERASE
Organism(s): Nakaseomyces glabratus CBS 138
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-05-14 Released: 2013-05-29
Deposition Author(s): Shankar, M., Wilbanks, S.M., Nakatani, Y., Monk, B.C., Tyndall, J.D.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free:
0.252 (Depositor), 0.236 (DCC)
R-Value Work:
0.200 (Depositor)
R-Value Observed:
0.201 (Depositor)

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

Catalysis product captured in lumazine synthase from the fungal pathogen Candida glabrata.

Shankar, M., Wilbanks, S.M., Nakatani, Y., Monk, B.C., Tyndall, J.D.

(2013) Acta Crystallogr D Biol Crystallogr 69: 1580-1586

PubMed: 23897480 Search on PubMed
DOI: https://doi.org/10.1107/S0907444913010949
Primary Citation Related Structures:
4KQ6

PubMed Abstract:
Candida glabrata has emerged as an important fungal pathogen with intrinsic resistance to azole drugs. The limited efficacy of and resistance to existing antifungals is driving the need to identify new drug targets. The enzyme 6,7-dimethyl-8-(D-ribityl)lumazine synthase is part of the riboflavin-biosynthesis pathway essential to fungi and bacteria and is a potential drug target for the development of broad-spectrum antifungal drugs. The X-ray crystal structure of recombinant lumazine synthase from C. glabrata was obtained at 2.24 Å resolution and revealed a dimer of homopentamers, with one in five subunits containing a product molecule from the catalytic reaction.

Organizational Affiliation

School of Pharmacy, University of Otago, PO Box 56, Dunedin 9054, New Zealand.

Macromolecule Content

Total Structure Weight: 199.16 kDa
Atom Count: 13,313
Modeled Residue Count: 1,586
Deposited Residue Count: 1,790
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6,7-dimethyl-8-ribityllumazine synthase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	179	Nakaseomyces glabratus CBS 138	Mutation(s): 0 Gene Names: CAGL0B01419g, RIB4 EC: 2.5.1.78
UniProt
Find proteins for Q6FXA8 (Candida glabrata (strain ATCC 2001 / BCRC 20586 / JCM 3761 / NBRC 0622 / NRRL Y-65 / CBS 138)) Explore Q6FXA8 Go to UniProtKB: Q6FXA8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6FXA8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DLZ Query on DLZ Download:Ideal Coordinates CCD File SDF format, chain KA [auth I] SDF format, chain R [auth C] MOL2 format, chain KA [auth I] MOL2 format, chain R [auth C] mmCIF format, chain KA [auth I] mmCIF format, chain R [auth C]	KA [auth I], R [auth C]	1-deoxy-1-(6,7-dimethyl-2,4-dioxo-3,4-dihydropteridin-8(2H)-yl)-D-ribitol C₁₃ H₁₈ N₄ O₆ SXDXRJZUAJBNFL-XKSSXDPKSA-N		Interactions Focus chain KA [auth I] Focus chain R [auth C] Interactions & Density Focus chain KA [auth I] Focus chain R [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain BA [auth G] SDF format, chain CA [auth G] SDF format, chain DA [auth G] SDF format, chain FA [auth H] SDF format, chain GA [auth H] SDF format, chain HA [auth I] SDF format, chain IA [auth I] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth J] SDF format, chain M [auth B] SDF format, chain MA [auth J] SDF format, chain N [auth B] SDF format, chain NA [auth J] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain S [auth D] SDF format, chain T [auth D] SDF format, chain V [auth E] SDF format, chain W [auth E] SDF format, chain Z [auth F] SDF format, chain Y [auth F] MOL2 format, chain AA [auth F] MOL2 format, chain BA [auth G] MOL2 format, chain CA [auth G] MOL2 format, chain DA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain GA [auth H] MOL2 format, chain HA [auth I] MOL2 format, chain IA [auth I] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth J] MOL2 format, chain M [auth B] MOL2 format, chain MA [auth J] MOL2 format, chain N [auth B] MOL2 format, chain NA [auth J] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D] MOL2 format, chain V [auth E] MOL2 format, chain W [auth E] MOL2 format, chain Z [auth F] MOL2 format, chain Y [auth F] mmCIF format, chain AA [auth F] mmCIF format, chain BA [auth G] mmCIF format, chain CA [auth G] mmCIF format, chain DA [auth G] mmCIF format, chain FA [auth H] mmCIF format, chain GA [auth H] mmCIF format, chain HA [auth I] mmCIF format, chain IA [auth I] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth J] mmCIF format, chain M [auth B] mmCIF format, chain MA [auth J] mmCIF format, chain N [auth B] mmCIF format, chain NA [auth J] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain S [auth D] mmCIF format, chain T [auth D] mmCIF format, chain V [auth E] mmCIF format, chain W [auth E] mmCIF format, chain Z [auth F] mmCIF format, chain Y [auth F]	AA [auth F] BA [auth G] CA [auth G] DA [auth G] FA [auth H] AA [auth F], BA [auth G], CA [auth G], DA [auth G], FA [auth H], GA [auth H], HA [auth I], IA [auth I], K [auth A], L [auth A], LA [auth J], M [auth B], MA [auth J], N [auth B], NA [auth J], O [auth C], P [auth C], Q [auth C], S [auth D], T [auth D], V [auth E], W [auth E], Y [auth F], Z [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth F] Focus chain BA [auth G] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain GA [auth H] Focus chain HA [auth I] Focus chain IA [auth I] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth J] Focus chain M [auth B] Focus chain MA [auth J] Focus chain N [auth B] Focus chain NA [auth J] Focus chain O [auth C] 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 F] Focus chain BA [auth G] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain FA [auth H] Focus chain GA [auth H] Focus chain HA [auth I] Focus chain IA [auth I] Focus chain K [auth A] Focus chain L [auth A] Focus chain LA [auth J] Focus chain M [auth B] Focus chain MA [auth J] Focus chain N [auth B] Focus chain NA [auth J] Focus chain O [auth C] 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]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain EA [auth G] SDF format, chain JA [auth I] SDF format, chain OA [auth J] SDF format, chain U [auth D] SDF format, chain X [auth E] MOL2 format, chain EA [auth G] MOL2 format, chain JA [auth I] MOL2 format, chain OA [auth J] MOL2 format, chain U [auth D] MOL2 format, chain X [auth E] mmCIF format, chain EA [auth G] mmCIF format, chain JA [auth I] mmCIF format, chain OA [auth J] mmCIF format, chain U [auth D] mmCIF format, chain X [auth E]	EA [auth G], JA [auth I], OA [auth J], U [auth D], X [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth G] Focus chain JA [auth I] Focus chain OA [auth J] Focus chain U [auth D] Focus chain X [auth E] Interactions & Density Focus chain EA [auth G] Focus chain JA [auth I] Focus chain OA [auth J] Focus chain U [auth D] Focus chain X [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free: 0.252 (Depositor), 0.236 (DCC)
R-Value Work: 0.200 (Depositor)
R-Value Observed: 0.201 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.75	α = 90
b = 84.84	β = 90
c = 310.2	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-05-29

Deposition Author(s):

This entry supersedes: 4GEF

Revision History (Full details and data files)

Version 1.0: 2013-05-29
Type: Initial release
Version 1.1: 2013-08-28
Changes: Database references
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description