5ZN6

Crystal structure of GH31 alpha-xylosidase from a soil metagenome

PDB DOI: https://doi.org/10.2210/pdb5ZN6/pdb

Classification: HYDROLASE
Organism(s): soil metagenome
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2018-04-07 Released: 2019-04-10
Deposition Author(s): Matsuzawa, T., Nakamichi, Y., Watanabe, M., Yaoi, K.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.195
R-Value Work: 0.174
R-Value Observed: 0.175

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural insight into substrate specificity of alpha-xylosidase from a soil metagenome

Matsuzawa, T., Nakamichi, Y., Watanabe, M., Yaoi, K.

To be published.

Macromolecule Content

Total Structure Weight: 631.78 kDa
Atom Count: 47,599
Modelled Residue Count: 5,421
Deposited Residue Count: 5,496
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-xylosidase MeXyl31	A B C D E A, B, C, D, E, F, G [auth H], H [auth G]	687	soil metagenome	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain AB [auth H] SDF format, chain BA [auth C] SDF format, chain BB [auth H] SDF format, chain CA [auth C] SDF format, chain CB [auth G] SDF format, chain DA [auth C] SDF format, chain DB [auth G] SDF format, chain EA [auth C] SDF format, chain EB [auth G] SDF format, chain FA [auth C] SDF format, chain FB [auth G] SDF format, chain GA [auth C] SDF format, chain GB [auth G] SDF format, chain HA [auth D] SDF format, chain HB [auth G] SDF format, chain I [auth A] SDF format, chain IA [auth D] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain N [auth A] SDF format, chain NA [auth E] SDF format, chain O [auth A] SDF format, chain OA [auth E] SDF format, chain P [auth A] SDF format, chain PA [auth E] SDF format, chain Q [auth A] SDF format, chain QA [auth E] SDF format, chain R [auth B] SDF format, chain RA [auth E] SDF format, chain S [auth B] SDF format, chain SA [auth F] SDF format, chain T [auth B] SDF format, chain TA [auth F] SDF format, chain U [auth B] SDF format, chain UA [auth H] SDF format, chain V [auth B] SDF format, chain VA [auth H] SDF format, chain W [auth B] SDF format, chain WA [auth H] SDF format, chain X [auth B] SDF format, chain XA [auth H] SDF format, chain Y [auth B] SDF format, chain YA [auth H] SDF format, chain Z [auth C] SDF format, chain ZA [auth H] MOL2 format, chain AA [auth C] MOL2 format, chain AB [auth H] MOL2 format, chain BA [auth C] MOL2 format, chain BB [auth H] MOL2 format, chain CA [auth C] MOL2 format, chain CB [auth G] MOL2 format, chain DA [auth C] MOL2 format, chain DB [auth G] MOL2 format, chain EA [auth C] MOL2 format, chain EB [auth G] MOL2 format, chain FA [auth C] MOL2 format, chain FB [auth G] MOL2 format, chain GA [auth C] MOL2 format, chain GB [auth G] MOL2 format, chain HA [auth D] MOL2 format, chain HB [auth G] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth E] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth E] MOL2 format, chain R [auth B] MOL2 format, chain RA [auth E] MOL2 format, chain S [auth B] MOL2 format, chain SA [auth F] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth F] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth H] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth H] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth H] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth H] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth H] MOL2 format, chain Z [auth C] MOL2 format, chain ZA [auth H]	AA [auth C] AB [auth H] BA [auth C] BB [auth H] CA [auth C] AA [auth C], AB [auth H], BA [auth C], BB [auth H], CA [auth C], CB [auth G], DA [auth C], DB [auth G], EA [auth C], EB [auth G], FA [auth C], FB [auth G], GA [auth C], GB [auth G], HA [auth D], HB [auth G], I [auth A], IA [auth D], J [auth A], JA [auth D], K [auth A], KA [auth D], L [auth A], LA [auth D], M [auth A], MA [auth D], N [auth A], NA [auth E], O [auth A], OA [auth E], P [auth A], PA [auth E], Q [auth A], QA [auth E], R [auth B], RA [auth E], S [auth B], SA [auth F], T [auth B], TA [auth F], U [auth B], UA [auth H], V [auth B], VA [auth H], W [auth B], WA [auth H], X [auth B], XA [auth H], Y [auth B], YA [auth H], Z [auth C], ZA [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain AB [auth H] Focus chain BA [auth C] Focus chain BB [auth H] Focus chain CA [auth C] Focus chain CB [auth G] Focus chain DA [auth C] Focus chain DB [auth G] Focus chain EA [auth C] Focus chain EB [auth G] Focus chain FA [auth C] Focus chain FB [auth G] Focus chain GA [auth C] Focus chain GB [auth G] Focus chain HA [auth D] Focus chain HB [auth G] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth E] Focus chain O [auth A] Focus chain OA [auth E] Focus chain P [auth A] Focus chain PA [auth E] Focus chain Q [auth A] Focus chain QA [auth E] Focus chain R [auth B] Focus chain RA [auth E] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth F] Focus chain U [auth B] Focus chain UA [auth H] Focus chain V [auth B] Focus chain VA [auth H] Focus chain W [auth B] Focus chain WA [auth H] Focus chain X [auth B] Focus chain XA [auth H] Focus chain Y [auth B] Focus chain YA [auth H] Focus chain Z [auth C] Focus chain ZA [auth H] Interactions & Density Focus chain AA [auth C] Focus chain AB [auth H] Focus chain BA [auth C] Focus chain BB [auth H] Focus chain CA [auth C] Focus chain CB [auth G] Focus chain DA [auth C] Focus chain DB [auth G] Focus chain EA [auth C] Focus chain EB [auth G] Focus chain FA [auth C] Focus chain FB [auth G] Focus chain GA [auth C] Focus chain GB [auth G] Focus chain HA [auth D] Focus chain HB [auth G] Focus chain I [auth A] Focus chain IA [auth D] Focus chain J [auth A] Focus chain JA [auth D] Focus chain K [auth A] Focus chain KA [auth D] Focus chain L [auth A] Focus chain LA [auth D] Focus chain M [auth A] Focus chain MA [auth D] Focus chain N [auth A] Focus chain NA [auth E] Focus chain O [auth A] Focus chain OA [auth E] Focus chain P [auth A] Focus chain PA [auth E] Focus chain Q [auth A] Focus chain QA [auth E] Focus chain R [auth B] Focus chain RA [auth E] Focus chain S [auth B] Focus chain SA [auth F] Focus chain T [auth B] Focus chain TA [auth F] Focus chain U [auth B] Focus chain UA [auth H] Focus chain V [auth B] Focus chain VA [auth H] Focus chain W [auth B] Focus chain WA [auth H] Focus chain X [auth B] Focus chain XA [auth H] Focus chain Y [auth B] Focus chain YA [auth H] Focus chain Z [auth C] Focus chain ZA [auth H]