3QUM

Crystal structure of human prostate specific antigen (PSA) in Fab sandwich with a high affinity and a PCa selective antibody

PDB DOI: https://doi.org/10.2210/pdb3QUM/pdb

Classification: IMMUNE SYSTEM
Organism(s): Homo sapiens, Mus musculus
Mutation(s): No

Deposited: 2011-02-24 Released: 2011-11-09
Deposition Author(s): Stura, E.A., Muller, B.H., Michel, S., Ducancel, F.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.294
R-Value Work: 0.198
R-Value Observed: 0.203

wwPDB Validation 3D Report Full Report

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

Macromolecule Content

Total Structure Weight: 249.84 kDa
Atom Count: 17,606
Modelled Residue Count: 2,222
Deposited Residue Count: 2,224
Unique protein chains: 5

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prostate-specific antigen	A [auth P], F [auth Q]	237	Homo sapiens	Mutation(s): 0 EC: 3.4.21.77
UniProt & NIH Common Fund Data Resources
Find proteins for P07288 (Homo sapiens) Explore P07288 Go to UniProtKB: P07288
PHAROS: P07288 GTEx: ENSG00000142515
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07288
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 5D3D11 Light Chain	B [auth L], G [auth M]	219	Mus musculus	Mutation(s): 0
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 5D3D11 Heavy Chain	C [auth H], H [auth K]	219	Mus musculus	Mutation(s): 0
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 5D5A5 Light Chain	D [auth A], I [auth C]	218	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 5D5A5 Heavy Chain	E [auth B], J [auth D]	219	Mus musculus	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
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-alpha-D-mannopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	K [auth E]	15		N-Glycosylation	Interactions Focus chain K [auth E] Interactions & Density Focus chain K [auth E]
Glycosylation Resources
GlyTouCan: G87655FC GlyCosmos: G87655FC GlyGen: G87655FC

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose	L [auth F]	2		O-Glycosylation	Interactions Focus chain L [auth F] Interactions & Density Focus chain L [auth F]
Glycosylation Resources
GlyTouCan: G00031MO GlyCosmos: G00031MO GlyGen: G00031MO

Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	M [auth G]	15		N-Glycosylation	Interactions Focus chain M [auth G] Interactions & Density Focus chain M [auth G]
Glycosylation Resources
GlyTouCan: G67371LF GlyCosmos: G67371LF GlyGen: G67371LF

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 7
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900084 Query on PRD_900084	L [auth F]	Thomsen-Friedenreich antigen	Oligosaccharide / Antigen		Interactions Focus chain L [auth F] Interactions & Density Focus chain L [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.20 Å
R-Value Free: 0.294
R-Value Work: 0.198
R-Value Observed: 0.203
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.308	α = 90
b = 226.883	β = 96.51
c = 118.694	γ = 90

Software Package:

Software Name	Purpose
ProDC	data collection
MOLREP	phasing
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-11-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-11-09
Type: Initial release
Version 1.1: 2011-12-21
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-09-13
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary