4AVV | pdb_00004avv

Structure of CPHPC bound to Serum Amyloid P Component

PDB DOI: https://doi.org/10.2210/pdb4AVV/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2012-05-29 Released: 2013-06-19
Deposition Author(s): Kolstoe, S.E., Jenvey, M.C., Wood, S.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free:
0.175 (Depositor), 0.179 (DCC)
R-Value Work:
0.150 (Depositor), 0.157 (DCC)
R-Value Observed:
0.150 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Interaction of Serum Amyloid P Component with Hexanoyl Bis(D-Proline) (Cphpc)

Kolstoe, S.E., Jenvey, M.C., Purvis, A., Light, M.E., Thompson, D., Hughes, P., Pepys, M.B., Wood, S.P.

(2014) Acta Crystallogr D Biol Crystallogr 70: 2232

PubMed: 25084341 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1399004714013455
Primary Citation Related Structures:
4AVS, 4AVT, 4AVV, 4AYU

PubMed Abstract:
Under physiological conditions, the pentameric human plasma protein serum amyloid P component (SAP) binds hexanoyl bis(D-proline) (R-1-{6-[R-2-carboxy-pyrrolidin-1-yl]-6-oxo-hexanoyl}pyrrolidine-2-carboxylic acid; CPHPC) through its D-proline head groups in a calcium-dependent interaction. Cooperative effects in binding lead to a substantial enhancement of affinity. Five molecules of the bivalent ligand cross-link and stabilize pairs of SAP molecules, forming a decameric complex that is rapidly cleared from the circulation by the liver. Here, it is reported that X-ray analysis of the SAP complex with CPHPC and cadmium ions provides higher resolution detail of the interaction than is observed with calcium ions. Conformational isomers of CPHPC observed in solution by HPLC and by X-ray analysis are compared with the protein-bound form. These are discussed in relation to the development of CPHPC to provide SAP depletion for the treatment of amyloidosis and other indications.

Organizational Affiliation

Laboratory of Protein Crystallography, Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins, Division of Medicine (Royal Free Campus), University College London, Rowland Hill Street, London NW3 2PF, England.

Macromolecule Content

Total Structure Weight: 126.14 kDa
Atom Count: 10,255
Modeled Residue Count: 1,020
Deposited Residue Count: 1,020
Unique protein chains: 1

Macromolecules

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| 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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02743
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E	Go to GlyGen: P02743-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	2		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	11		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G84467IZ GlyCosmos: G84467IZ GlyGen: G84467IZ

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GHE Query on GHE Download:Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain NA [auth D] SDF format, chain UA [auth E] SDF format, chain V [auth B] SDF format, chain HA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain NA [auth D] MOL2 format, chain UA [auth E] MOL2 format, chain V [auth B] MOL2 format, chain HA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain NA [auth D] mmCIF format, chain UA [auth E] mmCIF format, chain V [auth B] mmCIF format, chain HA [auth C]	HA [auth C], J [auth A], NA [auth D], UA [auth E], V [auth B]	(2R)-1-[6-[(2R)-2-carboxypyrrolidin-1-yl]-6-oxidanylidene-hexanoyl]pyrrolidine-2-carboxylic acid C₁₆ H₂₄ N₂ O₆ HZLAWYIBLZNRFZ-VXGBXAGGSA-N		Interactions Focus chain HA [auth C] Focus chain J [auth A] Focus chain NA [auth D] Focus chain UA [auth E] Focus chain V [auth B] Interactions & Density Focus chain HA [auth C] Focus chain J [auth A] Focus chain NA [auth D] Focus chain UA [auth E] Focus chain V [auth B]
SIA Query on SIA Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain BA [auth B]	BA [auth B]	N-acetyl-alpha-neuraminic acid C₁₁ H₁₉ N O₉ SQVRNKJHWKZAKO-YRMXFSIDSA-N		Interactions Focus chain BA [auth B] Interactions & Density Focus chain BA [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain JA [auth C] SDF format, chain Q [auth A] SDF format, chain AB [auth E] MOL2 format, chain JA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain AB [auth E] mmCIF format, chain JA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain AB [auth E]	AB [auth E], JA [auth C], Q [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AB [auth E] Focus chain JA [auth C] Focus chain Q [auth A] Interactions & Density Focus chain AB [auth E] Focus chain JA [auth C] Focus chain Q [auth A]
CD Query on CD Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain DB [auth E] SDF format, chain EA [auth B] SDF format, chain EB [auth E] SDF format, chain FA [auth C] SDF format, chain FB [auth E] SDF format, chain GA [auth C] SDF format, chain GB [auth E] SDF format, chain IA [auth C] SDF format, chain KA [auth C] SDF format, chain L [auth A] SDF format, chain LA [auth C] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth D] SDF format, chain P [auth A] SDF format, chain PA [auth D] SDF format, chain RA [auth D] SDF format, chain S [auth A] SDF format, chain SA [auth D] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain VA [auth E] SDF format, chain WA [auth E] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain YA [auth E] SDF format, chain Z [auth B] SDF format, chain ZA [auth E] SDF format, chain XA [auth E] SDF format, chain QA [auth D] SDF format, chain MA [auth C] SDF format, chain M [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth E] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth E] MOL2 format, chain FA [auth C] MOL2 format, chain FB [auth E] MOL2 format, chain GA [auth C] MOL2 format, chain GB [auth E] MOL2 format, chain IA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth D] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain VA [auth E] MOL2 format, chain WA [auth E] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth E] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth E] MOL2 format, chain XA [auth E] MOL2 format, chain QA [auth D] MOL2 format, chain MA [auth C] MOL2 format, chain M [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain DB [auth E] mmCIF format, chain EA [auth B] mmCIF format, chain EB [auth E] mmCIF format, chain FA [auth C] mmCIF format, chain FB [auth E] mmCIF format, chain GA [auth C] mmCIF format, chain GB [auth E] mmCIF format, chain IA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth D] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain RA [auth D] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth D] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain VA [auth E] mmCIF format, chain WA [auth E] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth E] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth E] mmCIF format, chain XA [auth E] mmCIF format, chain QA [auth D] mmCIF format, chain MA [auth C] mmCIF format, chain M [auth A]	AA [auth B] CA [auth B] DA [auth B] DB [auth E] EA [auth B] AA [auth B], CA [auth B], DA [auth B], DB [auth E], EA [auth B], EB [auth E], FA [auth C], FB [auth E], GA [auth C], GB [auth E], IA [auth C], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], O [auth A], OA [auth D], P [auth A], PA [auth D], QA [auth D], RA [auth D], S [auth A], SA [auth D], T [auth A], U [auth A], VA [auth E], WA [auth E], X [auth B], XA [auth E], Y [auth B], YA [auth E], Z [auth B], ZA [auth E]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain DB [auth E] Focus chain EA [auth B] Focus chain EB [auth E] Focus chain FA [auth C] Focus chain FB [auth E] Focus chain GA [auth C] Focus chain GB [auth E] Focus chain IA [auth C] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain S [auth A] Focus chain SA [auth D] Focus chain T [auth A] Focus chain U [auth A] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain X [auth B] Focus chain XA [auth E] Focus chain Y [auth B] Focus chain YA [auth E] Focus chain Z [auth B] Focus chain ZA [auth E] Interactions & Density Focus chain AA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain DB [auth E] Focus chain EA [auth B] Focus chain EB [auth E] Focus chain FA [auth C] Focus chain FB [auth E] Focus chain GA [auth C] Focus chain GB [auth E] Focus chain IA [auth C] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth D] Focus chain P [auth A] Focus chain PA [auth D] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain S [auth A] Focus chain SA [auth D] Focus chain T [auth A] Focus chain U [auth A] Focus chain VA [auth E] Focus chain WA [auth E] Focus chain X [auth B] Focus chain XA [auth E] Focus chain Y [auth B] Focus chain YA [auth E] Focus chain Z [auth B] Focus chain ZA [auth E]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain BB [auth E] SDF format, chain CB [auth E] SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain R [auth A] SDF format, chain TA [auth E] SDF format, chain W [auth B] SDF format, chain H [auth A] MOL2 format, chain BB [auth E] MOL2 format, chain CB [auth E] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain R [auth A] MOL2 format, chain TA [auth E] MOL2 format, chain W [auth B] MOL2 format, chain H [auth A] mmCIF format, chain BB [auth E] mmCIF format, chain CB [auth E] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain R [auth A] mmCIF format, chain TA [auth E] mmCIF format, chain W [auth B] mmCIF format, chain H [auth A]	BB [auth E] CB [auth E] H [auth A] I [auth A] K [auth A] BB [auth E], CB [auth E], H [auth A], I [auth A], K [auth A], R [auth A], TA [auth E], W [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain BB [auth E] Focus chain CB [auth E] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain R [auth A] Focus chain TA [auth E] Focus chain W [auth B] Interactions & Density Focus chain BB [auth E] Focus chain CB [auth E] Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Focus chain R [auth A] Focus chain TA [auth E] Focus chain W [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.175 (Depositor), 0.179 (DCC)
R-Value Work: 0.150 (Depositor), 0.157 (DCC)
R-Value Observed: 0.150 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.379	α = 90
b = 108.579	β = 138.53
c = 120.263	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-06-19

Deposition Author(s):

Kolstoe, S.E.

Jenvey, M.C.

Wood, S.P.

Revision History (Full details and data files)

Version 1.0: 2013-06-19
Type: Initial release
Version 1.1: 2014-08-06
Changes: Database references
Version 1.2: 2014-10-22
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
Version 2.1: 2023-12-20
Changes: Data collection, Database references, Refinement description, Structure summary
Version 2.2: 2024-11-13
Changes: Structure summary