8PN5

Crystal structure of the HC7-Glu200Ala mutant complexed to a triglycopeptide

PDB DOI: https://doi.org/10.2210/pdb8PN5/pdb

Classification: CARBOHYDRATE
Organism(s): Bacillus cereus, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-06-29 Released: 2024-03-06
Deposition Author(s): Taleb, V., Hurtado-Guerrero, R.
Funding Organization(s): Spanish Ministry of Economy and Competitiveness

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free: 0.235
R-Value Work: 0.208

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A family of di-glutamate mucin-degrading enzymes that bridges glycan hydrolases and peptidases

Narimatsu, Y., Bull, C., Taleb, V., Liao, Q., Companon, I., Sanchez-Navarro, D., Durbesson, F., Vincentelli, R., Hansen, L., Corzana, F., Rovira, C., Henrissat, B., Clausen, H., Joshi, H.J., Hurtado-Guerrero, R.

(2024) Nat Catal

DOI: https://doi.org/10.1038/s41929-024-01116-5

Macromolecule Content

Total Structure Weight: 582.18 kDa
Atom Count: 25,304
Modelled Residue Count: 2,835
Deposited Residue Count: 5,136
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DUF3472 domain-containing protein	A, B, C, D, E A, B, C, D, E, F, G, H	627	Bacillus cereus	Mutation(s): 0 Gene Names: DN401_14795
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Triglycopeptide	I, J, K, L, M I, J, K, L, M, N, O, P	15	synthetic construct	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A2G Query on A2G Download Ideal Coordinates CCD File SDF format, chain BB [auth N] SDF format, chain DB [auth O] SDF format, chain FB [auth O] SDF format, chain MA [auth I] SDF format, chain QA [auth J] SDF format, chain TA [auth K] SDF format, chain UA [auth L] SDF format, chain AB [auth N] SDF format, chain CB [auth N] SDF format, chain EB [auth O] SDF format, chain GB [auth P] SDF format, chain HB [auth P] SDF format, chain IB [auth P] SDF format, chain LA [auth I] SDF format, chain NA [auth I] SDF format, chain OA [auth J] SDF format, chain PA [auth J] SDF format, chain RA [auth K] SDF format, chain SA [auth K] SDF format, chain VA [auth L] SDF format, chain WA [auth L] SDF format, chain XA [auth M] SDF format, chain YA [auth M] SDF format, chain ZA [auth M] MOL2 format, chain BB [auth N] MOL2 format, chain DB [auth O] MOL2 format, chain FB [auth O] MOL2 format, chain MA [auth I] MOL2 format, chain QA [auth J] MOL2 format, chain TA [auth K] MOL2 format, chain UA [auth L] MOL2 format, chain AB [auth N] MOL2 format, chain CB [auth N] MOL2 format, chain EB [auth O] MOL2 format, chain GB [auth P] MOL2 format, chain HB [auth P] MOL2 format, chain IB [auth P] MOL2 format, chain LA [auth I] MOL2 format, chain NA [auth I] MOL2 format, chain OA [auth J] MOL2 format, chain PA [auth J] MOL2 format, chain RA [auth K] MOL2 format, chain SA [auth K] MOL2 format, chain VA [auth L] MOL2 format, chain WA [auth L] MOL2 format, chain XA [auth M] MOL2 format, chain YA [auth M] MOL2 format, chain ZA [auth M] mmCIF format, chain BB [auth N] mmCIF format, chain DB [auth O] mmCIF format, chain FB [auth O] mmCIF format, chain MA [auth I] mmCIF format, chain QA [auth J] mmCIF format, chain TA [auth K] mmCIF format, chain UA [auth L] mmCIF format, chain AB [auth N] mmCIF format, chain CB [auth N] mmCIF format, chain EB [auth O] mmCIF format, chain GB [auth P] mmCIF format, chain HB [auth P] mmCIF format, chain IB [auth P] mmCIF format, chain LA [auth I] mmCIF format, chain NA [auth I] mmCIF format, chain OA [auth J] mmCIF format, chain PA [auth J] mmCIF format, chain RA [auth K] mmCIF format, chain SA [auth K] mmCIF format, chain VA [auth L] mmCIF format, chain WA [auth L] mmCIF format, chain XA [auth M] mmCIF format, chain YA [auth M] mmCIF format, chain ZA [auth M]	AB [auth N] BB [auth N] CB [auth N] DB [auth O] EB [auth O] AB [auth N], BB [auth N], CB [auth N], DB [auth O], EB [auth O], FB [auth O], GB [auth P], HB [auth P], IB [auth P], LA [auth I], MA [auth I], NA [auth I], OA [auth J], PA [auth J], QA [auth J], RA [auth K], SA [auth K], TA [auth K], UA [auth L], VA [auth L], WA [auth L], XA [auth M], YA [auth M], ZA [auth M]	2-acetamido-2-deoxy-alpha-D-galactopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-CBQIKETKSA-N		Interactions Focus chain AB [auth N] Focus chain BB [auth N] Focus chain CB [auth N] Focus chain DB [auth O] Focus chain EB [auth O] Focus chain FB [auth O] Focus chain GB [auth P] Focus chain HB [auth P] Focus chain IB [auth P] Focus chain LA [auth I] Focus chain MA [auth I] Focus chain NA [auth I] Focus chain OA [auth J] Focus chain PA [auth J] Focus chain QA [auth J] Focus chain RA [auth K] Focus chain SA [auth K] Focus chain TA [auth K] Focus chain UA [auth L] Focus chain VA [auth L] Focus chain WA [auth L] Focus chain XA [auth M] Focus chain YA [auth M] Focus chain ZA [auth M] Interactions & Density Focus chain AB [auth N] Focus chain BB [auth N] Focus chain CB [auth N] Focus chain DB [auth O] Focus chain EB [auth O] Focus chain FB [auth O] Focus chain GB [auth P] Focus chain HB [auth P] Focus chain IB [auth P] Focus chain LA [auth I] Focus chain MA [auth I] Focus chain NA [auth I] Focus chain OA [auth J] Focus chain PA [auth J] Focus chain QA [auth J] Focus chain RA [auth K] Focus chain SA [auth K] Focus chain TA [auth K] Focus chain UA [auth L] Focus chain VA [auth L] Focus chain WA [auth L] Focus chain XA [auth M] Focus chain YA [auth M] Focus chain ZA [auth M]
MES Query on MES Download Ideal Coordinates CCD File SDF format, chain BA [auth F] MOL2 format, chain BA [auth F] mmCIF format, chain BA [auth F]	BA [auth F]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain BA [auth F] Interactions & Density Focus chain BA [auth F]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain EA [auth G] SDF format, chain HA [auth H] SDF format, chain IA [auth H] SDF format, chain JA [auth H] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain T [auth B] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth D] SDF format, chain Y [auth E] MOL2 format, chain AA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain HA [auth H] MOL2 format, chain IA [auth H] MOL2 format, chain JA [auth H] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain T [auth B] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth E] mmCIF format, chain AA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain HA [auth H] mmCIF format, chain IA [auth H] mmCIF format, chain JA [auth H] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain T [auth B] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain X [auth D] mmCIF format, chain Y [auth E]	AA [auth F] EA [auth G] HA [auth H] IA [auth H] JA [auth H] AA [auth F], EA [auth G], HA [auth H], IA [auth H], JA [auth H], Q [auth A], R [auth A], T [auth B], V [auth C], W [auth C], X [auth D], Y [auth E]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain Q [auth A] Focus chain R [auth A] Focus chain T [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth D] Focus chain Y [auth E] Interactions & Density Focus chain AA [auth F] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain IA [auth H] Focus chain JA [auth H] Focus chain Q [auth A] Focus chain R [auth A] Focus chain T [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth D] Focus chain Y [auth E]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain CA [auth F] SDF format, chain DA [auth F] SDF format, chain FA [auth G] SDF format, chain GA [auth G] SDF format, chain KA [auth H] SDF format, chain S [auth A] SDF format, chain U [auth B] SDF format, chain Z [auth E] MOL2 format, chain CA [auth F] MOL2 format, chain DA [auth F] MOL2 format, chain FA [auth G] MOL2 format, chain GA [auth G] MOL2 format, chain KA [auth H] MOL2 format, chain S [auth A] MOL2 format, chain U [auth B] MOL2 format, chain Z [auth E] mmCIF format, chain CA [auth F] mmCIF format, chain DA [auth F] mmCIF format, chain FA [auth G] mmCIF format, chain GA [auth G] mmCIF format, chain KA [auth H] mmCIF format, chain S [auth A] mmCIF format, chain U [auth B] mmCIF format, chain Z [auth E]	CA [auth F] DA [auth F] FA [auth G] GA [auth G] KA [auth H] CA [auth F], DA [auth F], FA [auth G], GA [auth G], KA [auth H], S [auth A], U [auth B], Z [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain CA [auth F] Focus chain DA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain KA [auth H] Focus chain S [auth A] Focus chain U [auth B] Focus chain Z [auth E] Interactions & Density Focus chain CA [auth F] Focus chain DA [auth F] Focus chain FA [auth G] Focus chain GA [auth G] Focus chain KA [auth H] Focus chain S [auth A] Focus chain U [auth B] Focus chain Z [auth E]