2WUC

Crystal structure of HGFA in complex with the allosteric non- inhibitory antibody Fab40.deltaTrp and Ac-KQLR-chloromethylketone

PDB DOI: https://doi.org/10.2210/pdb2WUC/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Homo sapiens, synthetic construct
Expression System: Trichoplusia ni, Escherichia coli
Mutation(s): No

Deposited: 2009-10-01 Released: 2009-12-15
Deposition Author(s): Ganesan, R., Eigenbrot, C., Shia, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.274
R-Value Work: 0.226
R-Value Observed: 0.226

wwPDB Validation 3D Report Full Report

This is version 3.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 79.8 kDa
Atom Count: 5,319
Modelled Residue Count: 686
Deposited Residue Count: 736
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HEPATOCYTE GROWTH FACTOR ACTIVATOR LONG CHAIN	A	257	Homo sapiens	Mutation(s): 0 EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q04756 (Homo sapiens) Explore Q04756 Go to UniProtKB: Q04756
PHAROS: Q04756 GTEx: ENSG00000109758
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q04756
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HEPATOCYTE GROWTH FACTOR ACTIVATOR SHORT CHAIN	B	35	Homo sapiens	Mutation(s): 0 EC: 3.4.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q04756 (Homo sapiens) Explore Q04756 Go to UniProtKB: Q04756
PHAROS: Q04756 GTEx: ENSG00000109758
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q04756
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
FAB FRAGMENT FAB40.DELTATRP HEAVY CHAIN	C [auth H]	224	Homo sapiens	Mutation(s): 0
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
ACE-KQLR-CHLOROMETHYLKETONE INHIBITOR	D [auth I]	6	synthetic construct	Mutation(s): 0
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
FAB FRAGMENT FAB40.DELTATRP LIGHT CHAIN	E [auth L]	214	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F [auth C]	2		N-Glycosylation	Interactions Focus chain F [auth C] Interactions & Density Focus chain F [auth C]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
AR7 Query on AR7	D [auth I]	PEPTIDE-LIKE	C₆ H₁₇ N₄ O₂		ARG

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000307 Query on PRD_000307	D [auth I]	N-acetyl-6-ammonio-L-norleucyl-L-glutaminyl-N-[(1S)-4-{[amino(iminio)methyl]amino}-1-(chloroacetyl)butyl]-L-leucinamide	Peptide-like / Inhibitor		Interactions Focus chain D [auth I] Interactions & Density Focus chain D [auth I]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.274
R-Value Work: 0.226
R-Value Observed: 0.226
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.359	α = 90
b = 147.889	β = 90
c = 146.371	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALA	data scaling
PHENIX	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-12-15

Deposition Author(s):

Ganesan, R.

Eigenbrot, C.

Shia, S.

Revision History (Full details and data files)

Version 1.0: 2009-12-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
Version 1.2: 2012-06-06
Changes: Other
Version 1.3: 2013-03-06
Changes: Other
Version 1.4: 2016-12-21
Changes: Source and taxonomy
Version 2.0: 2020-07-01
Changes: Advisory, Atomic model, Data collection, Derived calculations, Other
Version 3.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 3.1: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary