3ALA | pdb_00003ala

Crystal structure of vascular adhesion protein-1 in space group C2

PDB DOI: https://doi.org/10.2210/pdb3ALA/pdb

Classification: OXIDOREDUCTASE
Organism(s): Homo sapiens
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2010-07-29 Released: 2010-12-15
Deposition Author(s): Ernberg, K.E., McGrath, A.P., Guss, J.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.286 (Depositor), 0.282 (DCC)
R-Value Work:
0.250 (Depositor), 0.249 (DCC)
R-Value Observed:
0.252 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A new crystal form of human vascular adhesion protein 1

Ernberg, K., McGrath, A.P., Peat, T.S., Adams, T.E., Xiao, X., Pham, T., Newman, J., McDonald, I.A., Collyer, C.A., Guss, J.M.

(2010) Acta Crystallogr Sect F Struct Biol Cryst Commun 66: 1572-1578

PubMed: 21139198 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1107/S1744309110041515
Primary Citation Related Structures:
3ALA

PubMed Abstract:
Human vascular adhesion protein 1 (VAP-1) is involved in lymphocyte-endothelial cell adhesion and has been implicated in many human inflammatory diseases. VAP-1 is a member of the copper amine oxidase family of enzymes with a trihydroxyphenylalanine quinone (TPQ) cofactor. Previously characterized crystals of VAP-1 suffered from anisotropy and contained disordered regions; in addition, one form was consistently twinned. In an effort to grow crystals that diffracted to higher resolution for inhibitor-binding studies, a construct with an N-terminal deletion was made and expressed in the Chinese hamster ovary (CHO) glycosylation mutant cell line Lec8. Screening produced crystals that displayed some anisotropy and contained seven molecules per asymmetric unit. These crystals belonged to space group C2, with unit-cell parameters a=394.5, b=115.8, c=179.3 Å, β=112.3°. The structure was refined to a resolution of 2.9 Å, with Rcryst and Rfree values of 0.250 and 0.286, respectively.

Organizational Affiliation

School of Molecular Bioscience, University of Sydney, NSW 2006, Australia.

Macromolecule Content

Total Structure Weight: 595.58 kDa
Atom Count: 39,103
Modeled Residue Count: 4,939
Deposited Residue Count: 5,236
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Membrane primary amine oxidase	A, B, C, D, E A, B, C, D, E, F, G	748	Homo sapiens	Mutation(s): 0 Gene Names: AOC3, VAP1 EC: 1.4.3.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q16853 (Homo sapiens) Explore Q16853 Go to UniProtKB: Q16853
PHAROS: Q16853 GTEx: ENSG00000131471
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q16853
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G	Go to GlyGen: Q16853-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H, K, M, P, S H, K, M, P, S, V, Y	3		N-Glycosylation	Interactions Focus chain H Focus chain K Focus chain M Focus chain P Focus chain S Focus chain V Focus chain Y Interactions & Density Focus chain H Focus chain K Focus chain M Focus chain P Focus chain S Focus chain V Focus chain Y
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

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

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	J, O, R, U, X	2		N-Glycosylation	Interactions Focus chain J Focus chain O Focus chain R Focus chain U Focus chain X Interactions & Density Focus chain J Focus chain O Focus chain R Focus chain U Focus chain X
Glycosylation Resources
GlyTouCan: G61843VN GlyCosmos: G61843VN GlyGen: G61843VN

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	L	3		N-Glycosylation	Interactions Focus chain L Interactions & Density Focus chain L
Glycosylation Resources
GlyTouCan: G28454KX GlyCosmos: G28454KX GlyGen: G28454KX

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	AA [auth a]	2		N-Glycosylation	Interactions Focus chain AA [auth a] Interactions & Density Focus chain AA [auth a]
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain PA [auth D] SDF format, chain IA [auth B] MOL2 format, chain PA [auth D] MOL2 format, chain IA [auth B] mmCIF format, chain PA [auth D] mmCIF format, chain IA [auth B]	IA [auth B], PA [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain IA [auth B] Focus chain PA [auth D] Interactions & Density Focus chain IA [auth B] Focus chain PA [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain EA [auth A] MOL2 format, chain EA [auth A] mmCIF format, chain EA [auth A]	EA [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain EA [auth A] Interactions & Density Focus chain EA [auth A]
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain FA [auth B] SDF format, chain WA [auth G] SDF format, chain TA [auth F] SDF format, chain QA [auth E] SDF format, chain MA [auth D] SDF format, chain JA [auth C] SDF format, chain BA [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain WA [auth G] MOL2 format, chain TA [auth F] MOL2 format, chain QA [auth E] MOL2 format, chain MA [auth D] MOL2 format, chain JA [auth C] MOL2 format, chain BA [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain WA [auth G] mmCIF format, chain TA [auth F] mmCIF format, chain QA [auth E] mmCIF format, chain MA [auth D] mmCIF format, chain JA [auth C] mmCIF format, chain BA [auth A]	BA [auth A] FA [auth B] JA [auth C] MA [auth D] QA [auth E] BA [auth A], FA [auth B], JA [auth C], MA [auth D], QA [auth E], TA [auth F], WA [auth G]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Focus chain FA [auth B] Focus chain JA [auth C] Focus chain MA [auth D] Focus chain QA [auth E] Focus chain TA [auth F] Focus chain WA [auth G] Interactions & Density Focus chain BA [auth A] Focus chain FA [auth B] Focus chain JA [auth C] Focus chain MA [auth D] Focus chain QA [auth E] Focus chain TA [auth F] Focus chain WA [auth G]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain HA [auth B] SDF format, chain YA [auth G] SDF format, chain XA [auth G] SDF format, chain VA [auth F] SDF format, chain UA [auth F] SDF format, chain SA [auth E] SDF format, chain RA [auth E] SDF format, chain OA [auth D] SDF format, chain NA [auth D] SDF format, chain LA [auth C] SDF format, chain KA [auth C] SDF format, chain GA [auth B] SDF format, chain DA [auth A] SDF format, chain CA [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain YA [auth G] MOL2 format, chain XA [auth G] MOL2 format, chain VA [auth F] MOL2 format, chain UA [auth F] MOL2 format, chain SA [auth E] MOL2 format, chain RA [auth E] MOL2 format, chain OA [auth D] MOL2 format, chain NA [auth D] MOL2 format, chain LA [auth C] MOL2 format, chain KA [auth C] MOL2 format, chain GA [auth B] MOL2 format, chain DA [auth A] MOL2 format, chain CA [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain YA [auth G] mmCIF format, chain XA [auth G] mmCIF format, chain VA [auth F] mmCIF format, chain UA [auth F] mmCIF format, chain SA [auth E] mmCIF format, chain RA [auth E] mmCIF format, chain OA [auth D] mmCIF format, chain NA [auth D] mmCIF format, chain LA [auth C] mmCIF format, chain KA [auth C] mmCIF format, chain GA [auth B] mmCIF format, chain DA [auth A] mmCIF format, chain CA [auth A]	CA [auth A] DA [auth A] GA [auth B] HA [auth B] KA [auth C] CA [auth A], DA [auth A], GA [auth B], HA [auth B], KA [auth C], LA [auth C], NA [auth D], OA [auth D], RA [auth E], SA [auth E], UA [auth F], VA [auth F], XA [auth G], YA [auth G]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain CA [auth A] Focus chain DA [auth A] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain UA [auth F] Focus chain VA [auth F] Focus chain XA [auth G] Focus chain YA [auth G] Interactions & Density Focus chain CA [auth A] Focus chain DA [auth A] Focus chain GA [auth B] Focus chain HA [auth B] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain NA [auth D] Focus chain OA [auth D] Focus chain RA [auth E] Focus chain SA [auth E] Focus chain UA [auth F] Focus chain VA [auth F] Focus chain XA [auth G] Focus chain YA [auth G]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
TPQ Query on TPQ	A, B, C, D, E A, B, C, D, E, F, G	L-PEPTIDE LINKING	C₉ H₉ N O₅		TYR

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.286 (Depositor), 0.282 (DCC)
R-Value Work: 0.250 (Depositor), 0.249 (DCC)
R-Value Observed: 0.252 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 394.468	α = 90
b = 115.826	β = 112.34
c = 179.286	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2010-12-15

Deposition Author(s):

Ernberg, K.E.

McGrath, A.P.

Guss, J.M.

Revision History (Full details and data files)

Version 1.0: 2010-12-15
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2012-04-25
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-11-01
Changes: Advisory, Data collection, Database references, Refinement description, Structure summary

3ALA | pdb_00003ala

Crystal structure of vascular adhesion protein-1 in space group C2

Literature

A new crystal form of human vascular adhesion protein 1

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Glycosylation

Sequence Annotations

Expand

Oligosaccharides

Entity ID: 2

Glycosylation Resources

Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Entity ID: 5

Glycosylation Resources

Entity ID: 6

Glycosylation Resources

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Entry History

Deposition Data

Revision History (Full details and data files)