3BYW

Crystal structure of an extracellular domain of arabinofuranosyltransferase from Corynebacterium diphtheriae

PDB DOI: https://doi.org/10.2210/pdb3BYW/pdb

Classification: TRANSFERASE
Organism(s): Corynebacterium diphtheriae NCTC 13129
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2008-01-16 Released: 2008-02-19
Deposition Author(s): Tan, K., Hatzos, C., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free: 0.263
R-Value Work: 0.209
R-Value Observed: 0.212

wwPDB Validation 3D Report Full Report

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

Literature

The structure of an extracellular domain of arabinofuranosyltransferase from Corynebacterium diphtheriae.

Tan, K., Hatzos, C., Abdullah, J., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 152.57 kDa
Atom Count: 9,635
Modelled Residue Count: 1,269
Deposited Residue Count: 1,416
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative arabinofuranosyltransferase	A, B, C, D, E A, B, C, D, E, F, G, H	177	Corynebacterium diphtheriae NCTC 13129	Mutation(s): 0 Gene Names: DIP0159
UniProt
Find proteins for Q6NK78 (Corynebacterium diphtheriae (strain ATCC 700971 / NCTC 13129 / Biotype gravis)) Explore Q6NK78 Go to UniProtKB: Q6NK78
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6NK78
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain DA [auth E] SDF format, chain EA [auth E] SDF format, chain I [auth A] SDF format, chain IA [auth F] SDF format, chain J [auth A] SDF format, chain KA [auth G] SDF format, chain L [auth B] SDF format, chain LA [auth G] SDF format, chain N [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain CA [auth E] SDF format, chain JA [auth F] SDF format, chain M [auth B] MOL2 format, chain BA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth F] MOL2 format, chain J [auth A] MOL2 format, chain KA [auth G] MOL2 format, chain L [auth B] MOL2 format, chain LA [auth G] MOL2 format, chain N [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain JA [auth F] MOL2 format, chain M [auth B]	BA [auth E] CA [auth E] DA [auth E] EA [auth E] I [auth A] BA [auth E], CA [auth E], DA [auth E], EA [auth E], I [auth A], IA [auth F], J [auth A], JA [auth F], KA [auth G], L [auth B], LA [auth G], M [auth B], N [auth B], R [auth C], S [auth C], U [auth D], V [auth D], W [auth D], X [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain I [auth A] Focus chain IA [auth F] Focus chain J [auth A] Focus chain JA [auth F] Focus chain KA [auth G] Focus chain L [auth B] Focus chain LA [auth G] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth E] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain I [auth A] Focus chain IA [auth F] Focus chain J [auth A] Focus chain JA [auth F] Focus chain KA [auth G] Focus chain L [auth B] Focus chain LA [auth G] Focus chain M [auth B] Focus chain N [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain FA [auth E] SDF format, chain GA [auth E] SDF format, chain HA [auth E] SDF format, chain K [auth A] SDF format, chain MA [auth G] SDF format, chain NA [auth H] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain T [auth C] SDF format, chain Y [auth D] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain GA [auth E] MOL2 format, chain HA [auth E] MOL2 format, chain K [auth A] MOL2 format, chain MA [auth G] MOL2 format, chain NA [auth H] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth C] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D]	AA [auth D] FA [auth E] GA [auth E] HA [auth E] K [auth A] AA [auth D], FA [auth E], GA [auth E], HA [auth E], K [auth A], MA [auth G], NA [auth H], O [auth B], P [auth B], Q [auth B], T [auth C], Y [auth D], Z [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain K [auth A] Focus chain MA [auth G] Focus chain NA [auth H] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain HA [auth E] Focus chain K [auth A] Focus chain MA [auth G] Focus chain NA [auth H] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain T [auth C] Focus chain Y [auth D] Focus chain Z [auth D]