6X91

Crystal structure of MBP-fused human APOBEC1

PDB DOI: https://doi.org/10.2210/pdb6X91/pdb

Classification: HYDROLASE
Organism(s): Escherichia coli, Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2020-06-02 Released: 2020-12-09
Deposition Author(s): Wolfe, A.D., Li, S.-X., Chen, X.S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.51 Å
R-Value Free: 0.298
R-Value Work: 0.276
R-Value Observed: 0.278

wwPDB Validation 3D Report Full Report

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

Macromolecule Content

Total Structure Weight: 543 kDa
Atom Count: 37,624
Modelled Residue Count: 4,667
Deposited Residue Count: 4,744
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Maltodextrin-binding protein, C->U-editing enzyme APOBEC-1 chimera	A, B, C, D, E A, B, C, D, E, F, G, H	593	Escherichia coli, Homo sapiens This entity is chimeric	Mutation(s): 9 Gene Names: DAH37_23060, APOBEC1 EC: 3.5.4.36
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12)) Explore P0AEX9 Go to UniProtKB: P0AEX9
Find proteins for P41238 (Homo sapiens) Explore P41238 Go to UniProtKB: P41238
PHAROS: P41238 GTEx: ENSG00000111701
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P41238P0AEX9
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose	I, J, K, L, M I, J, K, L, M, N, O, P, Q, R, S, T, U, V	2		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 Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V 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 Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V
Glycosylation Resources
GlyTouCan: G07411ON GlyCosmos: G07411ON

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CAC Query on CAC Download Ideal Coordinates CCD File SDF format, chain BA [auth C] SDF format, chain DA [auth D] SDF format, chain FA [auth E] SDF format, chain HA [auth F] SDF format, chain JA [auth G] SDF format, chain LA [auth H] SDF format, chain X [auth A] SDF format, chain Z [auth B] MOL2 format, chain BA [auth C] MOL2 format, chain DA [auth D] MOL2 format, chain FA [auth E] MOL2 format, chain HA [auth F] MOL2 format, chain JA [auth G] MOL2 format, chain LA [auth H] MOL2 format, chain X [auth A] MOL2 format, chain Z [auth B]	BA [auth C] DA [auth D] FA [auth E] HA [auth F] JA [auth G] BA [auth C], DA [auth D], FA [auth E], HA [auth F], JA [auth G], LA [auth H], X [auth A], Z [auth B]	CACODYLATE ION C₂ H₆ As O₂ OGGXGZAMXPVRFZ-UHFFFAOYSA-M		Interactions Focus chain BA [auth C] Focus chain DA [auth D] Focus chain FA [auth E] Focus chain HA [auth F] Focus chain JA [auth G] Focus chain LA [auth H] Focus chain X [auth A] Focus chain Z [auth B] Interactions & Density Focus chain BA [auth C] Focus chain DA [auth D] Focus chain FA [auth E] Focus chain HA [auth F] Focus chain JA [auth G] Focus chain LA [auth H] Focus chain X [auth A] Focus chain Z [auth B]
ZN (Subject of Investigation/LOI) Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain CA [auth D] SDF format, chain EA [auth E] SDF format, chain GA [auth F] SDF format, chain IA [auth G] SDF format, chain KA [auth H] SDF format, chain W [auth A] SDF format, chain Y [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain CA [auth D] MOL2 format, chain EA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain IA [auth G] MOL2 format, chain KA [auth H] MOL2 format, chain W [auth A] MOL2 format, chain Y [auth B]	AA [auth C] CA [auth D] EA [auth E] GA [auth F] IA [auth G] AA [auth C], CA [auth D], EA [auth E], GA [auth F], IA [auth G], KA [auth H], W [auth A], Y [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain CA [auth D] Focus chain EA [auth E] Focus chain GA [auth F] Focus chain IA [auth G] Focus chain KA [auth H] Focus chain W [auth A] Focus chain Y [auth B] Interactions & Density Focus chain AA [auth C] Focus chain CA [auth D] Focus chain EA [auth E] Focus chain GA [auth F] Focus chain IA [auth G] Focus chain KA [auth H] Focus chain W [auth A] Focus chain Y [auth B]

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900001 Query on PRD_900001	I, J, K, L, M I, J, K, L, M, N, O, P, Q, R, S, T, U, V	alpha-maltose	Oligosaccharide / Nutrient		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 Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V 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 Focus chain Q Focus chain R Focus chain S Focus chain T Focus chain U Focus chain V