3NG9 | pdb_00003ng9

Structure to Function Correlations for Adeno-associated Virus Serotype 1

PDB DOI: https://doi.org/10.2210/pdb3NG9/pdb

Classification: VIRUS
Organism(s): Adeno-associated virus - 1
Mutation(s): No

Deposited: 2010-06-11 Released: 2011-12-21
Deposition Author(s): Govindasamy, L., Miller, E.B., Gurda, B., McKenna, R., Zolotukhin, S., Muzyczka, N., Agbandje-McKenna, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.250 (Depositor), 0.261 (DCC)
R-Value Work:
0.230 (Depositor), 0.257 (DCC)
R-Value Observed:
0.230 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Structure to Function Correlations for Adeno-Associated Virus serotype 1

Govindasamy, L., Miller, E.B., Gurda, B., McKenna, R., Zolotukhin, S., Muzyczka, N., Agbandje-McKenna, M.

To be published.

Macromolecule Content

Total Structure Weight: 817.01 kDa
Atom Count: 42,680
Modeled Residue Count: 5,200
Deposited Residue Count: 7,360
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A, B, C, D, E A, B, C, D, E, F, G, H, I, J	736	Adeno-associated virus - 1	Mutation(s): 0
UniProt
Find proteins for Q9WBP8 (Adeno-associated virus - 1) Explore Q9WBP8 Go to UniProtKB: Q9WBP8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WBP8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADE Query on ADE Download:Ideal Coordinates CCD File SDF format, chain AA [auth I] SDF format, chain K [auth A] SDF format, chain M [auth B] SDF format, chain V [auth F] SDF format, chain X [auth G] SDF format, chain Y [auth H] SDF format, chain T [auth E] SDF format, chain R [auth D] SDF format, chain P [auth C] SDF format, chain CA [auth J] MOL2 format, chain AA [auth I] MOL2 format, chain K [auth A] MOL2 format, chain M [auth B] MOL2 format, chain V [auth F] MOL2 format, chain X [auth G] MOL2 format, chain Y [auth H] MOL2 format, chain T [auth E] MOL2 format, chain R [auth D] MOL2 format, chain P [auth C] MOL2 format, chain CA [auth J] mmCIF format, chain AA [auth I] mmCIF format, chain K [auth A] mmCIF format, chain M [auth B] mmCIF format, chain V [auth F] mmCIF format, chain X [auth G] mmCIF format, chain Y [auth H] mmCIF format, chain T [auth E] mmCIF format, chain R [auth D] mmCIF format, chain P [auth C] mmCIF format, chain CA [auth J]	AA [auth I] CA [auth J] K [auth A] M [auth B] P [auth C] AA [auth I], CA [auth J], K [auth A], M [auth B], P [auth C], R [auth D], T [auth E], V [auth F], X [auth G], Y [auth H]	ADENINE C₅ H₅ N₅ GFFGJBXGBJISGV-UHFFFAOYSA-N		Interactions Focus chain AA [auth I] Focus chain CA [auth J] Focus chain K [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Y [auth H] Interactions & Density Focus chain AA [auth I] Focus chain CA [auth J] Focus chain K [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain V [auth F] Focus chain X [auth G] Focus chain Y [auth H]
CYT Query on CYT Download:Ideal Coordinates CCD File SDF format, chain BA [auth I] SDF format, chain L [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain Q [auth C] SDF format, chain U [auth E] SDF format, chain Z [auth H] SDF format, chain W [auth F] SDF format, chain S [auth D] SDF format, chain DA [auth J] MOL2 format, chain BA [auth I] MOL2 format, chain L [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain U [auth E] MOL2 format, chain Z [auth H] MOL2 format, chain W [auth F] MOL2 format, chain S [auth D] MOL2 format, chain DA [auth J] mmCIF format, chain BA [auth I] mmCIF format, chain L [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain U [auth E] mmCIF format, chain Z [auth H] mmCIF format, chain W [auth F] mmCIF format, chain S [auth D] mmCIF format, chain DA [auth J]	BA [auth I] DA [auth J] L [auth A] N [auth B] O [auth B] BA [auth I], DA [auth J], L [auth A], N [auth B], O [auth B], Q [auth C], S [auth D], U [auth E], W [auth F], Z [auth H]	6-AMINOPYRIMIDIN-2(1H)-ONE C₄ H₅ N₃ O OPTASPLRGRRNAP-UHFFFAOYSA-N		Interactions Focus chain BA [auth I] Focus chain DA [auth J] Focus chain L [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Z [auth H] Interactions & Density Focus chain BA [auth I] Focus chain DA [auth J] Focus chain L [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain Q [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Z [auth H]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.250 (Depositor), 0.261 (DCC)
R-Value Work: 0.230 (Depositor), 0.257 (DCC)
R-Value Observed: 0.230 (Depositor)

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 262.7	α = 90
b = 262.7	β = 90
c = 612.3	γ = 120

Software Package:

Software Name	Purpose
MAR345	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2011-12-21

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-12-21
Type: Initial release
Version 1.1: 2017-11-08
Changes: Refinement description
Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description