9A24 | pdb_00009a24

PTX3 hybrid cryoEM and AlphaFold model

Integrative structure models are generated using different types of input information, including varied experimental data, physical principles, statistical preferences, and other prior information.

PDB DOI: https://doi.org/10.2210/pdb9A24/pdb

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

Deposited: 2022-07-20 Released: 2022-07-29
Deposition Author(s): Dylan P. Noone, Thomas H. Sharp

Integrative Structure Snapshot

Multi-Scale: No
Multi-State: No
Ordered-State: No
Deposited Models: 1
Representative Model: 1

wwPDB ValidationFull ReportSummary Report

This is version 1.0 of the entry. See complete history.

Literature

PTX3 structure determination using a hybrid cryo-electron microscopy and AlphaFold approach offers insights into ligand binding and complement activation

Dylan P. Noone, Thomas H. Sharp

(2022) Proc Natl Acad Sci U S A

DOI: https://doi.org/10.1073/pnas.2208144119

Macromolecule Content

Total Structure Weight: 381.48 kDa
Atom Count: 23,383
Modeled Residue Count: 2,912
Deposited Residue Count: 2,912
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PTX3 (protein complex)	A [auth B] B [auth A] C [auth D] D [auth C] E [auth F] A [auth B], B [auth A], C [auth D], D [auth C], E [auth F], F [auth E], G [auth H], H [auth G]	364	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P26022 (Homo sapiens) Explore P26022 Go to UniProtKB: P26022
PHAROS: P26022 GTEx: ENSG00000163661
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P26022
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 Y [auth C] SDF format, chain X [auth C] SDF format, chain W [auth D] SDF format, chain SA [auth G] SDF format, chain S [auth D] SDF format, chain RA [auth G] SDF format, chain O [auth A] SDF format, chain NA [auth H] SDF format, chain N [auth A] SDF format, chain MA [auth H] SDF format, chain J [auth B] SDF format, chain IA [auth E] SDF format, chain I [auth B] SDF format, chain HA [auth E] SDF format, chain DA [auth F] SDF format, chain CA [auth F] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain W [auth D] MOL2 format, chain SA [auth G] MOL2 format, chain S [auth D] MOL2 format, chain RA [auth G] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth H] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth H] MOL2 format, chain J [auth B] MOL2 format, chain IA [auth E] MOL2 format, chain I [auth B] MOL2 format, chain HA [auth E] MOL2 format, chain DA [auth F] MOL2 format, chain CA [auth F] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain W [auth D] mmCIF format, chain SA [auth G] mmCIF format, chain S [auth D] mmCIF format, chain RA [auth G] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth H] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth H] mmCIF format, chain J [auth B] mmCIF format, chain IA [auth E] mmCIF format, chain I [auth B] mmCIF format, chain HA [auth E] mmCIF format, chain DA [auth F] mmCIF format, chain CA [auth F]	CA [auth F] DA [auth F] HA [auth E] I [auth B] IA [auth E] CA [auth F], DA [auth F], HA [auth E], I [auth B], IA [auth E], J [auth B], MA [auth H], N [auth A], NA [auth H], O [auth A], RA [auth G], S [auth D], SA [auth G], W [auth D], X [auth C], Y [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain CA [auth F] Focus chain DA [auth F] Focus chain HA [auth E] Focus chain I [auth B] Focus chain IA [auth E] Focus chain J [auth B] Focus chain MA [auth H] Focus chain N [auth A] Focus chain NA [auth H] Focus chain O [auth A] Focus chain RA [auth G] Focus chain S [auth D] Focus chain SA [auth G] Focus chain W [auth D] Focus chain X [auth C] Focus chain Y [auth C]
BMA Query on BMA Download:Ideal Coordinates CCD File SDF format, chain Z [auth C] SDF format, chain TA [auth G] SDF format, chain T [auth D] SDF format, chain P [auth A] SDF format, chain OA [auth H] SDF format, chain K [auth B] SDF format, chain JA [auth E] SDF format, chain EA [auth F] MOL2 format, chain Z [auth C] MOL2 format, chain TA [auth G] MOL2 format, chain T [auth D] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth H] MOL2 format, chain K [auth B] MOL2 format, chain JA [auth E] MOL2 format, chain EA [auth F] mmCIF format, chain Z [auth C] mmCIF format, chain TA [auth G] mmCIF format, chain T [auth D] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth H] mmCIF format, chain K [auth B] mmCIF format, chain JA [auth E] mmCIF format, chain EA [auth F]	EA [auth F] JA [auth E] K [auth B] OA [auth H] P [auth A] EA [auth F], JA [auth E], K [auth B], OA [auth H], P [auth A], T [auth D], TA [auth G], Z [auth C]	beta-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-RWOPYEJCSA-N		Interactions Focus chain EA [auth F] Focus chain JA [auth E] Focus chain K [auth B] Focus chain OA [auth H] Focus chain P [auth A] Focus chain T [auth D] Focus chain TA [auth G] Focus chain Z [auth C]
MAN Query on MAN Download:Ideal Coordinates CCD File SDF format, chain VA [auth G] SDF format, chain V [auth D] SDF format, chain UA [auth G] SDF format, chain U [auth D] SDF format, chain R [auth A] SDF format, chain QA [auth H] SDF format, chain Q [auth A] SDF format, chain PA [auth H] SDF format, chain M [auth B] SDF format, chain LA [auth E] SDF format, chain L [auth B] SDF format, chain KA [auth E] SDF format, chain GA [auth F] SDF format, chain FA [auth F] SDF format, chain BA [auth C] SDF format, chain AA [auth C] MOL2 format, chain VA [auth G] MOL2 format, chain V [auth D] MOL2 format, chain UA [auth G] MOL2 format, chain U [auth D] MOL2 format, chain R [auth A] MOL2 format, chain QA [auth H] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth H] MOL2 format, chain M [auth B] MOL2 format, chain LA [auth E] MOL2 format, chain L [auth B] MOL2 format, chain KA [auth E] MOL2 format, chain GA [auth F] MOL2 format, chain FA [auth F] MOL2 format, chain BA [auth C] MOL2 format, chain AA [auth C] mmCIF format, chain VA [auth G] mmCIF format, chain V [auth D] mmCIF format, chain UA [auth G] mmCIF format, chain U [auth D] mmCIF format, chain R [auth A] mmCIF format, chain QA [auth H] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth H] mmCIF format, chain M [auth B] mmCIF format, chain LA [auth E] mmCIF format, chain L [auth B] mmCIF format, chain KA [auth E] mmCIF format, chain GA [auth F] mmCIF format, chain FA [auth F] mmCIF format, chain BA [auth C] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth C] FA [auth F] GA [auth F] KA [auth E] AA [auth C], BA [auth C], FA [auth F], GA [auth F], KA [auth E], L [auth B], LA [auth E], M [auth B], PA [auth H], Q [auth A], QA [auth H], R [auth A], U [auth D], UA [auth G], V [auth D], VA [auth G]	alpha-D-mannopyranose C₆ H₁₂ O₆ WQZGKKKJIJFFOK-PQMKYFCFSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain FA [auth F] Focus chain GA [auth F] Focus chain KA [auth E] Focus chain L [auth B] Focus chain LA [auth E] Focus chain M [auth B] Focus chain PA [auth H] Focus chain Q [auth A] Focus chain QA [auth H] Focus chain R [auth A] Focus chain U [auth D] Focus chain UA [auth G] Focus chain V [auth D] Focus chain VA [auth G]