1Z32 | pdb_00001z32

Structure-function relationships in human salivary alpha-amylase: Role of aromatic residues

PDB DOI: https://doi.org/10.2210/pdb1Z32/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2005-03-10 Released: 2005-05-31
Deposition Author(s): Ramasubbu, N., Ragunath, C., Sundar, K., Mishra, P.J., Gyemant, G., Kandra, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.192 (Depositor), 0.190 (DCC)
R-Value Work:
0.171 (Depositor), 0.170 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.4 of the entry. See complete history.

Literature

Structure-function relationships in human salivary alpha-amylase: Role of aromatic residues

Ramasubbu, N., Ragunath, C., Sundar, K., Mishra, P.J., Gyemant, G., Kandra, L.

To be published.

Macromolecule Content

Total Structure Weight: 56.52 kDa
Atom Count: 4,315
Modeled 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
Salivary alpha-amylase	A [auth X]	496	Homo sapiens	Mutation(s): 1 Gene Names: AMY1A, AMY1 EC: 3.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for P0DUB6 (Homo sapiens) Explore P0DUB6 Go to UniProtKB: P0DUB6
GTEx: ENSG00000237763
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DUB6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GLC Query on GLC Download Ideal Coordinates CCD File SDF format, chain B [auth X] MOL2 format, chain B [auth X] mmCIF format, chain B [auth X]	B [auth X]	alpha-D-glucopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-DVKNGEFBSA-N		Interactions Focus chain B [auth X] Interactions & Density Focus chain B [auth X]
HMC Query on HMC Download Ideal Coordinates CCD File SDF format, chain D [auth X] MOL2 format, chain D [auth X] mmCIF format, chain D [auth X]	D [auth X]	5-HYDROXYMETHYL-CHONDURITOL C₇ H₁₂ O₅ PJPGMULJEYSZBS-VZFHVOOUSA-N		Interactions Focus chain D [auth X] Interactions & Density Focus chain D [auth X]
AGL Query on AGL Download Ideal Coordinates CCD File SDF format, chain C [auth X] MOL2 format, chain C [auth X] mmCIF format, chain C [auth X]	C [auth X]	4-amino-4,6-dideoxy-alpha-D-glucopyranose C₆ H₁₃ N O₄ RJKBJEZZABBYBA-DVKNGEFBSA-N		Interactions Focus chain C [auth X] Interactions & Density Focus chain C [auth X]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth X] MOL2 format, chain E [auth X] mmCIF format, chain E [auth X]	E [auth X]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth X] Interactions & Density Focus chain E [auth X]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain F [auth X] MOL2 format, chain F [auth X] mmCIF format, chain F [auth X]	F [auth X]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain F [auth X] Interactions & Density Focus chain F [auth X]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.192 (Depositor), 0.190 (DCC)
R-Value Work: 0.171 (Depositor), 0.170 (DCC)
R-Value Observed: 0.172 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.657	α = 90
b = 73.513	β = 90
c = 134.362	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-05-31

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-05-31
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2018-02-14
Changes: Advisory, Experimental preparation
Version 2.0: 2019-12-25
Changes: Data collection, Database references, Derived calculations, Polymer sequence
Version 2.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Structure summary
Version 2.2: 2021-10-20
Changes: Database references, Structure summary
Version 2.3: 2023-08-23
Changes: Data collection, Refinement description
Version 2.4: 2024-11-13
Changes: Structure summary