6TAV | pdb_00006tav

Crystal structure of endopeptidase-induced alpha2-macroglobulin

PDB DOI: https://doi.org/10.2210/pdb6TAV/pdb
Entry: 6TAV supersedes: 4ACQ

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2019-10-30 Released: 2021-05-12
Deposition Author(s): Gomis-Ruth, F.X., Duquerroy, S., Trapani, S., Marrero, A., Goulas, T., Guevara, T., Andersen, G.A., Sottrup-Jensen, L., Navaza, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 4.20 Å
R-Value Free:
0.282 (Depositor), 0.290 (DCC)
R-Value Work:
0.235 (Depositor), 0.270 (DCC)
R-Value Observed:
0.236 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Cryo-EM structures shows the mechanistic basis of pan-peptidase inhibition by human alpha2-macroglobulin

Luque, D., Goulas, T., Mata, C.P., Mendes, S.R., Gomis-Ruth, F.X., Caston, J.R.

(2022) Proc Natl Acad Sci U S A

Macromolecule Content

Total Structure Weight: 666.2 kDa
Atom Count: 41,633
Modelled Residue Count: 5,234
Deposited Residue Count: 5,896
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-2-macroglobulin	A, B, C, D	1,474	Homo sapiens	Mutation(s): 0 Gene Names: A2M, CPAMD5, FWP007
UniProt & NIH Common Fund Data Resources
Find proteins for P01023 (Homo sapiens) Explore P01023 Go to UniProtKB: P01023
PHAROS: P01023 GTEx: ENSG00000175899
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01023
Glycosylation
Glycosylation Sites: 8	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: P01023-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
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	E, G, J, O, V	4		N-Glycosylation	Interactions Focus chain E Focus chain G Focus chain J Focus chain O Focus chain V Interactions & Density Focus chain E Focus chain G Focus chain J Focus chain O Focus chain V
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, I, M, R	3		N-Glycosylation	Interactions Focus chain F Focus chain I Focus chain M Focus chain R Interactions & Density Focus chain F Focus chain I Focus chain M Focus chain R
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H, K, L, N, P H, K, L, N, P, Q, S, T, U	2		N-Glycosylation	Interactions Focus chain H Focus chain K Focus chain L Focus chain N Focus chain P Focus chain Q Focus chain S Focus chain T Focus chain U Interactions & Density Focus chain H Focus chain K Focus chain L Focus chain N Focus chain P Focus chain Q Focus chain S Focus chain T Focus chain U
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain DA [auth C] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain GA [auth D] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain Z [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain GA [auth D] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth C] mmCIF format, chain CA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain GA [auth D] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain Z [auth B]	AA [auth C] BA [auth C] CA [auth C] DA [auth C] EA [auth D] AA [auth C], BA [auth C], CA [auth C], DA [auth C], EA [auth D], FA [auth D], GA [auth D], W [auth A], X [auth A], Y [auth A], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain DA [auth C] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain GA [auth D] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth B]