2OXC

Human DEAD-box RNA helicase DDX20, DEAD domain in complex with ADP

PDB DOI: https://doi.org/10.2210/pdb2OXC/pdb

Deposited: 2007-02-20 Released: 2007-02-27
Deposition Author(s): Karlberg, T., Ogg, D., Arrowsmith, C.H., Berglund, H., Busam, R.D., Collins, R., Dahlgren, L.G., Edwards, A., Flodin, S., Flores, A., Graslund, S., Hallberg, B.M., Hammarstrom, M., Hogbom, M., Johansson, I., Kotenyova, T., Lehtio, L., Moche, M., Nordlund, P., Nyman, T., Persson, C., Sagemark, J., Stenmark, P., Sundstrom, M., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Holmberg-Schiavone, L., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free:
0.175 (Depositor), 0.190 (DCC)
R-Value Work:
0.153 (Depositor), 0.160 (DCC)
R-Value Observed:
0.154 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Human DEAD-box RNA helicase DDX20

Karlberg, T., Ogg, D., H Arrowsmith, C., Berglund, H., Busam, R.D., Collins, R., Dahlgren, L.G., Edwards, A., Flodin, S., Flores, A., Graslund, S., Hallberg, B.M., Hammarstrom, M., Hogbom, M., Johansson, I., Kotenyova, T., Lehtio, L., Moche, M., Nordlund, P., Nyman, T., Persson, C., Sagemark, J., Stenmark, P., Sundstrom, M., Thorsell, A.G., Van Den Berg, S., Weigelt, J., Holmberg-Schiavone, L.

To be published.

Macromolecule Content

Total Structure Weight: 51.21 kDa
Atom Count: 3,949
Modelled Residue Count: 410
Deposited Residue Count: 460
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable ATP-dependent RNA helicase DDX20	A, B	230	Homo sapiens	Mutation(s): 0 Gene Names: DDX20, DP103, GEMIN3 EC: 3.6.1 (PDB Primary Data), 3.6.4.13 (UniProt), 3.6.1.15 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHI6 (Homo sapiens) Explore Q9UHI6 Go to UniProtKB: Q9UHI6
PHAROS: Q9UHI6 GTEx: ENSG00000064703
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9UHI6
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.175 (Depositor), 0.190 (DCC)
R-Value Work: 0.153 (Depositor), 0.160 (DCC)
R-Value Observed: 0.154 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.8	α = 90
b = 63.8	β = 90
c = 214.3	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
XDS	data reduction
XDS	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2007-02-27

Deposition Author(s):

Holmberg-Schiavone, L.

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2007-02-27
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2018-01-24
Changes: Structure summary
Version 1.5: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description