2W08

The structure of serum amyloid P component bound to 0-phospho- threonine

PDB DOI: https://doi.org/10.2210/pdb2W08/pdb

Classification: GLYCOPROTEIN
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2008-08-12 Released: 2009-04-14
Deposition Author(s): Kolstoe, S.E., Pepys, M.B., Wood, S.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.176
R-Value Work: 0.154
R-Value Observed: 0.154

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 118.91 kDa
Atom Count: 9,910
Modelled Residue Count: 1,020
Deposited Residue Count: 1,020
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERUM AMYLOID P-COMPONENT	A, B, C, D, E	204	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P02743 (Homo sapiens) Explore P02743 Go to UniProtKB: P02743
PHAROS: P02743 GTEx: ENSG00000132703
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02743
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 H [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] SDF format, chain T [auth D] SDF format, chain X [auth E] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C] MOL2 format, chain T [auth D] MOL2 format, chain X [auth E]	H [auth A], L [auth B], P [auth C], T [auth D], X [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain X [auth E] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain T [auth D] Focus chain X [auth E]
TPO Query on TPO Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain U [auth D] SDF format, chain Y [auth E] MOL2 format, chain I [auth A] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth D] MOL2 format, chain Y [auth E]	I [auth A], M [auth B], Q [auth C], U [auth D], Y [auth E]	PHOSPHOTHREONINE C₄ H₁₀ N O₆ P USRGIUJOYOXOQJ-GBXIJSLDSA-N		Interactions Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain Y [auth E] Interactions & Density Focus chain I [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain U [auth D] Focus chain Y [auth E]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain O [auth C] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain V [auth E] SDF format, chain W [auth E] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain V [auth E] MOL2 format, chain W [auth E]	F [auth A] G [auth A] J [auth B] K [auth B] N [auth C] F [auth A], G [auth A], J [auth B], K [auth B], N [auth C], O [auth C], R [auth D], S [auth D], V [auth E], W [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain V [auth E] Focus chain W [auth E] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Focus chain S [auth D] Focus chain V [auth E] Focus chain W [auth E]

Binding Affinity Annotations
ID	Source	Binding Affinity
TPO	Binding MOAD: 2W08	Kd: 3.80e+5 (nM) from 1 assay(s)
TPO	PDBBind: 2W08	Kd: 3.80e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.176
R-Value Work: 0.154
R-Value Observed: 0.154
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.769	α = 90
b = 69.435	β = 97.05
c = 102.063	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-04-14

Deposition Author(s):

Kolstoe, S.E.

Pepys, M.B.

Wood, S.P.

Revision History (Full details and data files)

Version 1.0: 2009-04-14
Type: Initial release
Version 1.1: 2011-05-07
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Data collection, Derived calculations, Other, Structure summary
Version 1.4: 2023-12-13
Changes: Data collection, Database references, Refinement description, Structure summary