1KBK

Mechanistic Analyses of Catalysis in Human Pancreatic Alpha-Amylase: Detailed Kinetic and Structural Studies of Mutants of Three Conserved Carboxylic Acids

PDB DOI: https://doi.org/10.2210/pdb1KBK/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Komagataella pastoris
Mutation(s): Yes

Deposited: 2001-11-06 Released: 2002-04-10
Deposition Author(s): Rydberg, E.H., Li, C., Maurus, R., Overall, C.M., Brayer, G.D., Withers, S.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.177
R-Value Work: 0.171

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 56.18 kDa
Atom Count: 4,097
Modelled Residue Count: 496
Deposited Residue Count: 496
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA-AMYLASE, PANCREATIC	A	496	Homo sapiens	Mutation(s): 1 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [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 D [auth A] MOL2 format, chain D [auth A]	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [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: 1.90 Å
R-Value Free: 0.177
R-Value Work: 0.171
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.88	α = 90
b = 69.52	β = 90
c = 131.6	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2002-04-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2002-04-10
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 2.0: 2019-12-25
Changes: Database references, Derived calculations, Polymer sequence
Version 2.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 2.2: 2021-10-27
Changes: Database references, Structure summary

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1KBK

Mechanistic Analyses of Catalysis in Human Pancreatic Alpha-Amylase: Detailed Kinetic and Structural Studies of Mutants of Three Conserved Carboxylic Acids

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)