8FK4

Structure of the catalytic domain of Streptococcus mutans GtfB complexed to acarbose in orthorhombic space group P21212

PDB DOI: https://doi.org/10.2210/pdb8FK4/pdb

Classification: TRANSFERASE
Organism(s): Streptococcus mutans
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-12-20 Released: 2023-05-17
Deposition Author(s): Schormann, N., Deivanayagam, C.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.25 Å
R-Value Free: 0.255
R-Value Work: 0.224
R-Value Observed: 0.225

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The catalytic domains of Streptococcus mutans glucosyltransferases: a structural analysis

Schormann, N., Patel, M., Thannickal, L., Purushotham, S., Wu, R., Mieher, J.L., Wu, H., Deivanayagam, C.

(2023) Acta Crystallogr F Struct Biol Commun 79: 119-127

DOI: https://doi.org/10.1107/S2053230X23003199

Macromolecule Content

Total Structure Weight: 789.51 kDa
Atom Count: 52,614
Modelled Residue Count: 6,604
Deposited Residue Count: 6,952
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosyltransferase-I	A, B, C, D, E A, B, C, D, E, F, G, H	869	Streptococcus mutans	Mutation(s): 0 Gene Names: gtfB, SMU_1004 EC: 2.4.1.5
UniProt
Find proteins for P08987 (Streptococcus mutans serotype c (strain ATCC 700610 / UA159)) Explore P08987 Go to UniProtKB: P08987
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08987
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	I, J, K, L, M I, J, K, L, M, N, O, P	3	N/A	N/A	Interactions Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Interactions & Density Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P
Glycosylation Resources
GlyTouCan: G66431MI GlyCosmos: G66431MI

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 (Subject of Investigation/LOI) Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth F] SDF format, chain BA [auth B] SDF format, chain BB [auth F] SDF format, chain CA [auth B] SDF format, chain CB [auth F] SDF format, chain DA [auth B] SDF format, chain DB [auth F] SDF format, chain EA [auth B] SDF format, chain EB [auth F] SDF format, chain FB [auth F] SDF format, chain GA [auth C] SDF format, chain HA [auth C] SDF format, chain HB [auth G] SDF format, chain IA [auth C] SDF format, chain IB [auth G] SDF format, chain JA [auth C] SDF format, chain JB [auth G] SDF format, chain KA [auth C] SDF format, chain KB [auth G] SDF format, chain MA [auth D] SDF format, chain MB [auth H] SDF format, chain NA [auth D] SDF format, chain OA [auth D] SDF format, chain PA [auth D] SDF format, chain QA [auth D] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain SA [auth E] SDF format, chain T [auth A] SDF format, chain TA [auth E] SDF format, chain U [auth A] SDF format, chain UA [auth E] SDF format, chain V [auth A] SDF format, chain VA [auth E] SDF format, chain W [auth A] SDF format, chain WA [auth E] SDF format, chain XA [auth E] SDF format, chain Y [auth B] SDF format, chain YA [auth E] SDF format, chain Z [auth B] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth F] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth F] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth F] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth F] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth F] MOL2 format, chain FB [auth F] MOL2 format, chain GA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain HB [auth G] MOL2 format, chain IA [auth C] MOL2 format, chain IB [auth G] MOL2 format, chain JA [auth C] MOL2 format, chain JB [auth G] MOL2 format, chain KA [auth C] MOL2 format, chain KB [auth G] MOL2 format, chain MA [auth D] MOL2 format, chain MB [auth H] MOL2 format, chain NA [auth D] MOL2 format, chain OA [auth D] MOL2 format, chain PA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth E] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth E] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth E] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth E] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth E] MOL2 format, chain XA [auth E] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth E] MOL2 format, chain Z [auth B]	AA [auth B] AB [auth F] BA [auth B] BB [auth F] CA [auth B] AA [auth B], AB [auth F], BA [auth B], BB [auth F], CA [auth B], CB [auth F], DA [auth B], DB [auth F], EA [auth B], EB [auth F], FB [auth F], GA [auth C], HA [auth C], HB [auth G], IA [auth C], IB [auth G], JA [auth C], JB [auth G], KA [auth C], KB [auth G], MA [auth D], MB [auth H], NA [auth D], OA [auth D], PA [auth D], QA [auth D], R [auth A], S [auth A], SA [auth E], T [auth A], TA [auth E], U [auth A], UA [auth E], V [auth A], VA [auth E], W [auth A], WA [auth E], XA [auth E], Y [auth B], YA [auth E], Z [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth B] Focus chain AB [auth F] Focus chain BA [auth B] Focus chain BB [auth F] Focus chain CA [auth B] Focus chain CB [auth F] Focus chain DA [auth B] Focus chain DB [auth F] Focus chain EA [auth B] Focus chain EB [auth F] Focus chain FB [auth F] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain HB [auth G] Focus chain IA [auth C] Focus chain IB [auth G] Focus chain JA [auth C] Focus chain JB [auth G] Focus chain KA [auth C] Focus chain KB [auth G] Focus chain MA [auth D] Focus chain MB [auth H] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain R [auth A] Focus chain S [auth A] Focus chain SA [auth E] Focus chain T [auth A] Focus chain TA [auth E] Focus chain U [auth A] Focus chain UA [auth E] Focus chain V [auth A] Focus chain VA [auth E] Focus chain W [auth A] Focus chain WA [auth E] Focus chain XA [auth E] Focus chain Y [auth B] Focus chain YA [auth E] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth F] Focus chain BA [auth B] Focus chain BB [auth F] Focus chain CA [auth B] Focus chain CB [auth F] Focus chain DA [auth B] Focus chain DB [auth F] Focus chain EA [auth B] Focus chain EB [auth F] Focus chain FB [auth F] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain HB [auth G] Focus chain IA [auth C] Focus chain IB [auth G] Focus chain JA [auth C] Focus chain JB [auth G] Focus chain KA [auth C] Focus chain KB [auth G] Focus chain MA [auth D] Focus chain MB [auth H] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain R [auth A] Focus chain S [auth A] Focus chain SA [auth E] Focus chain T [auth A] Focus chain TA [auth E] Focus chain U [auth A] Focus chain UA [auth E] Focus chain V [auth A] Focus chain VA [auth E] Focus chain W [auth A] Focus chain WA [auth E] Focus chain XA [auth E] Focus chain Y [auth B] Focus chain YA [auth E] Focus chain Z [auth B]
CA (Subject of Investigation/LOI) Query on CA Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain GB [auth G] SDF format, chain LA [auth D] SDF format, chain LB [auth H] SDF format, chain Q [auth A] SDF format, chain RA [auth E] SDF format, chain X [auth B] SDF format, chain ZA [auth F] MOL2 format, chain FA [auth C] MOL2 format, chain GB [auth G] MOL2 format, chain LA [auth D] MOL2 format, chain LB [auth H] MOL2 format, chain Q [auth A] MOL2 format, chain RA [auth E] MOL2 format, chain X [auth B] MOL2 format, chain ZA [auth F]	FA [auth C] GB [auth G] LA [auth D] LB [auth H] Q [auth A] FA [auth C], GB [auth G], LA [auth D], LB [auth H], Q [auth A], RA [auth E], X [auth B], ZA [auth F]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain FA [auth C] Focus chain GB [auth G] Focus chain LA [auth D] Focus chain LB [auth H] Focus chain Q [auth A] Focus chain RA [auth E] Focus chain X [auth B] Focus chain ZA [auth F] Interactions & Density Focus chain FA [auth C] Focus chain GB [auth G] Focus chain LA [auth D] Focus chain LB [auth H] Focus chain Q [auth A] Focus chain RA [auth E] Focus chain X [auth B] Focus chain ZA [auth F]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900007 Query on PRD_900007	I, J, K, L, M I, J, K, L, M, N, O, P	alpha-acarbose	Oligosaccharide / Inhibitor		Interactions Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P Interactions & Density Focus chain I Focus chain J Focus chain K Focus chain L Focus chain M Focus chain N Focus chain O Focus chain P