1Z68

Crystal Structure Of Human Fibroblast Activation Protein alpha

PDB DOI: https://doi.org/10.2210/pdb1Z68/pdb

Classification: LYASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2005-03-21 Released: 2005-04-12
Deposition Author(s): Aertgeerts, K., Levin, I., Shi, L., Prasad, G.S., Zhang, Y., Kraus, M.L., Salakian, S., Snell, G.P., Sridhar, V., Wijnands, R., Tennant, M.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.283
R-Value Work: 0.223
R-Value Observed: 0.226

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 169.17 kDa
Atom Count: 12,600
Modelled Residue Count: 1,438
Deposited Residue Count: 1,438
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
fibroblast activation protein, alpha subunit	A, B	719	Homo sapiens	Mutation(s): 0 EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q12884 (Homo sapiens) Explore Q12884 Go to UniProtKB: Q12884
PHAROS: Q12884 GTEx: ENSG00000078098
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q12884
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C, E	2		N-Glycosylation	Interactions Focus chain C Focus chain E Interactions & Density Focus chain C Focus chain E
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G79924RM GlyCosmos: G79924RM GlyGen: G79924RM

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 F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B]	F [auth A] G [auth A] H [auth B] I [auth B] J [auth B] F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.283
R-Value Work: 0.223
R-Value Observed: 0.226
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.295	α = 90
b = 152.58	β = 90
c = 214.855	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-04-12

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-04-12
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Advisory, Version format compliance
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-08-23
Changes: Data collection, Database references, Refinement description, Structure summary

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Deposit Data

Help and Resources

1Z68

Crystal Structure Of Human Fibroblast Activation Protein alpha

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Entity ID: 2

Glycosylation Resources