1NLX | pdb_00001nlx

Crystal Structure of PHL P 6, A Major Timothy Grass Pollen Allergen Co-Crystallized with Zinc

PDB DOI: https://doi.org/10.2210/pdb1NLX/pdb

Classification: ALLERGEN
Organism(s): Phleum pratense
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2003-01-07 Released: 2003-01-21
Deposition Author(s): Fedorov, A.A., Ball, T., Fedorov, E.V., Vrtala, S., Valenta, R., Almo, S.C., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free:
0.272 (Depositor), 0.270 (DCC)
R-Value Work:
0.243 (Depositor), 0.240 (DCC)
R-Value Observed:
0.248 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structure oh Phl p 6, a major timothy grass pollen allergen co-crystallized with Zinc

Fedorov, A.A., Ball, T., Fedorov, E.V., Vrtala, S., Valenta, R., Almo, S.C.

To be published.

Macromolecule Content

Total Structure Weight: 169.47 kDa
Atom Count: 11,151
Modeled Residue Count: 1,456
Deposited Residue Count: 1,554
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Pollen allergen Phl p 6	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	111	Phleum pratense	Mutation(s): 0 Gene Names: PHLPVI
UniProt
Find proteins for P43215 (Phleum pratense) Explore P43215 Go to UniProtKB: P43215
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P43215
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ARS Query on ARS Download Ideal Coordinates CCD File SDF format, chain JA [auth I] SDF format, chain OA [auth K] SDF format, chain RA [auth L] SDF format, chain S [auth B] SDF format, chain V [auth C] SDF format, chain WA [auth N] SDF format, chain Y [auth D] MOL2 format, chain JA [auth I] MOL2 format, chain OA [auth K] MOL2 format, chain RA [auth L] MOL2 format, chain S [auth B] MOL2 format, chain V [auth C] MOL2 format, chain WA [auth N] MOL2 format, chain Y [auth D] mmCIF format, chain JA [auth I] mmCIF format, chain OA [auth K] mmCIF format, chain RA [auth L] mmCIF format, chain S [auth B] mmCIF format, chain V [auth C] mmCIF format, chain WA [auth N] mmCIF format, chain Y [auth D]	JA [auth I] OA [auth K] RA [auth L] S [auth B] V [auth C] JA [auth I], OA [auth K], RA [auth L], S [auth B], V [auth C], WA [auth N], Y [auth D]	ARSENIC As RBFQJDQYXXHULB-UHFFFAOYSA-N		Interactions Focus chain JA [auth I] Focus chain OA [auth K] Focus chain RA [auth L] Focus chain S [auth B] Focus chain V [auth C] Focus chain WA [auth N] Focus chain Y [auth D] Interactions & Density Focus chain JA [auth I] Focus chain OA [auth K] Focus chain RA [auth L] Focus chain S [auth B] Focus chain V [auth C] Focus chain WA [auth N] Focus chain Y [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth E] SDF format, chain BA [auth F] SDF format, chain CA [auth F] SDF format, chain DA [auth G] SDF format, chain EA [auth G] SDF format, chain FA [auth H] SDF format, chain GA [auth H] SDF format, chain HA [auth I] SDF format, chain IA [auth I] SDF format, chain KA [auth J] SDF format, chain LA [auth J] SDF format, chain MA [auth K] SDF format, chain NA [auth K] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain PA [auth L] SDF format, chain Q [auth B] SDF format, chain QA [auth L] SDF format, chain R [auth B] SDF format, chain SA [auth M] SDF format, chain T [auth C] SDF format, chain TA [auth M] SDF format, chain U [auth C] SDF format, chain UA [auth N] SDF format, chain VA [auth N] SDF format, chain W [auth D] SDF format, chain X [auth D] SDF format, chain Z [auth E] MOL2 format, chain AA [auth E] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth F] MOL2 format, chain DA [auth G] MOL2 format, chain EA [auth G] MOL2 format, chain FA [auth H] MOL2 format, chain GA [auth H] MOL2 format, chain HA [auth I] MOL2 format, chain IA [auth I] MOL2 format, chain KA [auth J] MOL2 format, chain LA [auth J] MOL2 format, chain MA [auth K] MOL2 format, chain NA [auth K] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth L] MOL2 format, chain Q [auth B] MOL2 format, chain QA [auth L] MOL2 format, chain R [auth B] MOL2 format, chain SA [auth M] MOL2 format, chain T [auth C] MOL2 format, chain TA [auth M] MOL2 format, chain U [auth C] MOL2 format, chain UA [auth N] MOL2 format, chain VA [auth N] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] MOL2 format, chain Z [auth E] mmCIF format, chain AA [auth E] mmCIF format, chain BA [auth F] mmCIF format, chain CA [auth F] mmCIF format, chain DA [auth G] mmCIF format, chain EA [auth G] mmCIF format, chain FA [auth H] mmCIF format, chain GA [auth H] mmCIF format, chain HA [auth I] mmCIF format, chain IA [auth I] mmCIF format, chain KA [auth J] mmCIF format, chain LA [auth J] mmCIF format, chain MA [auth K] mmCIF format, chain NA [auth K] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth L] mmCIF format, chain Q [auth B] mmCIF format, chain QA [auth L] mmCIF format, chain R [auth B] mmCIF format, chain SA [auth M] mmCIF format, chain T [auth C] mmCIF format, chain TA [auth M] mmCIF format, chain U [auth C] mmCIF format, chain UA [auth N] mmCIF format, chain VA [auth N] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D] mmCIF format, chain Z [auth E]	AA [auth E] BA [auth F] CA [auth F] DA [auth G] EA [auth G] AA [auth E], BA [auth F], CA [auth F], DA [auth G], EA [auth G], FA [auth H], GA [auth H], HA [auth I], IA [auth I], KA [auth J], LA [auth J], MA [auth K], NA [auth K], O [auth A], P [auth A], PA [auth L], Q [auth B], QA [auth L], R [auth B], SA [auth M], T [auth C], TA [auth M], U [auth C], UA [auth N], VA [auth N], W [auth D], X [auth D], Z [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain GA [auth H] Focus chain HA [auth I] Focus chain IA [auth I] Focus chain KA [auth J] Focus chain LA [auth J] Focus chain MA [auth K] Focus chain NA [auth K] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth L] Focus chain Q [auth B] Focus chain QA [auth L] Focus chain R [auth B] Focus chain SA [auth M] Focus chain T [auth C] Focus chain TA [auth M] Focus chain U [auth C] Focus chain UA [auth N] Focus chain VA [auth N] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth E] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain FA [auth H] Focus chain GA [auth H] Focus chain HA [auth I] Focus chain IA [auth I] Focus chain KA [auth J] Focus chain LA [auth J] Focus chain MA [auth K] Focus chain NA [auth K] Focus chain O [auth A] Focus chain P [auth A] Focus chain PA [auth L] Focus chain Q [auth B] Focus chain QA [auth L] Focus chain R [auth B] Focus chain SA [auth M] Focus chain T [auth C] Focus chain TA [auth M] Focus chain U [auth C] Focus chain UA [auth N] Focus chain VA [auth N] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.272 (Depositor), 0.270 (DCC)
R-Value Work: 0.243 (Depositor), 0.240 (DCC)
R-Value Observed: 0.248 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.809	α = 90
b = 110.335	β = 90
c = 159.42	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2003-01-21

Deposition Author(s):

New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History (Full details and data files)

Version 1.0: 2003-01-21
Type: Initial release
Version 1.1: 2008-04-29
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2021-02-03
Changes: Database references, Derived calculations, Structure summary
Version 1.4: 2024-02-14
Changes: Data collection, Database references