6OBX

Montbretin A analogue M10-MbA in complex with Human pancreatic alpha-amylase

PDB DOI: https://doi.org/10.2210/pdb6OBX/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Komagataella pastoris
Mutation(s): No

Deposited: 2019-03-21 Released: 2020-02-12
Deposition Author(s): Caner, S., Brayer, G.D.
Funding Organization(s): Canadian Institutes of Health Research (CIHR)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.123
R-Value Work: 0.099
R-Value Observed: 0.100

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Re-refinement Note

This entry reflects an alternative modeling of the original data in: 5E0F 4W93 5U3A

Macromolecule Content

Total Structure Weight: 57.03 kDa
Atom Count: 4,632
Modelled Residue Count: 496
Deposited Residue Count: 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
Pancreatic alpha-amylase	A	496	Homo sapiens	Mutation(s): 0 Gene Names: AMY2A EC: 3.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04746 (Homo sapiens) Explore P04746 Go to UniProtKB: P04746
PHAROS: P04746 GTEx: ENSG00000243480
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04746
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZXU Query on ZXU Download Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A]	D [auth A]	N-(3-{[2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4-oxo-4H-1-benzopyran-3-yl]oxy}propyl)-Nalpha-[(2E)-3-(3,4-dihydroxyphenyl )prop-2-enoyl]-L-tyrosinamide C₃₆ H₃₂ N₂ O₁₂ IRVRXEMGBYHLMY-REHZOHHSSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on PCA	A	L-PEPTIDE LINKING	C₅ H₇ N O₃		GLN

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.123
R-Value Work: 0.099
R-Value Observed: 0.100
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.42	α = 90
b = 68.22	β = 90
c = 130.33	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2020-02-12

Deposition Author(s):

Caner, S.

Brayer, G.D.

Funding Organization	Location	Grant Number
Canadian Institutes of Health Research (CIHR)	Canada	CIHR MOP-111082

Revision History (Full details and data files)

Version 1.0: 2020-02-12
Type: Initial release
Version 1.1: 2020-04-15
Changes: Database references
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2023-10-11
Changes: Data collection, Database references, Refinement description, Structure summary