4L1M | pdb_00004l1m

Structure of the first RCC1-like domain of HERC2

PDB DOI: https://doi.org/10.2210/pdb4L1M/pdb

Classification: LIGASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2013-06-03 Released: 2013-07-03
Deposition Author(s): Tempel, W., Khan, M.B., Dong, A., Hu, J., Li, Y., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Tong, Y., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.238 (Depositor), 0.240 (DCC)
R-Value Work:
0.199 (Depositor), 0.210 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history.

Literature

Structure of the first RCC1-like domain of HERC2

Tempel, W., Khan, M.B., Dong, A., Hu, J., Li, Y., Bountra, C., Arrowsmith, C.H., Edwards, A.M., Tong, Y.

To be published.

Macromolecule Content

Total Structure Weight: 127.24 kDa
Atom Count: 7,981
Modeled Residue Count: 1,068
Deposited Residue Count: 1,176
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase HERC2	A, B, C	392	Homo sapiens	Mutation(s): 0 Gene Names: HERC2 EC: 6.3.2 (PDB Primary Data), 2.3.2.26 (UniProt)	👁 Image
UniProt & NIH Common Fund Data Resources
Find proteins for O95714 (Homo sapiens) Explore O95714 Go to UniProtKB: O95714
PHAROS: O95714 GTEx: ENSG00000128731
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O95714
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain IA [auth C] SDF format, chain HA [auth C] SDF format, chain GA [auth C] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain T [auth B] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain IA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain GA [auth C] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain T [auth B] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain IA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain GA [auth C] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] GA [auth C] D [auth A], E [auth A], F [auth A], G [auth A], GA [auth C], HA [auth C], IA [auth C], Q [auth B], R [auth B], S [auth B], T [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L	👁 Image	Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain GA [auth C] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B]
UNX Query on UNX Download Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain W [auth B] SDF format, chain VA [auth C] SDF format, chain V [auth B] SDF format, chain UA [auth C] SDF format, chain U [auth B] SDF format, chain TA [auth C] SDF format, chain SA [auth C] SDF format, chain RA [auth C] SDF format, chain QA [auth C] SDF format, chain PA [auth C] SDF format, chain P [auth A] SDF format, chain OA [auth C] SDF format, chain O [auth A] SDF format, chain NA [auth C] SDF format, chain N [auth A] SDF format, chain MA [auth C] SDF format, chain M [auth A] SDF format, chain LA [auth C] SDF format, chain L [auth A] SDF format, chain KA [auth C] SDF format, chain K [auth A] SDF format, chain JA [auth C] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain FA [auth B] SDF format, chain EA [auth B] SDF format, chain DA [auth B] SDF format, chain CA [auth B] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain VA [auth C] MOL2 format, chain V [auth B] MOL2 format, chain UA [auth C] MOL2 format, chain U [auth B] MOL2 format, chain TA [auth C] MOL2 format, chain SA [auth C] MOL2 format, chain RA [auth C] MOL2 format, chain QA [auth C] MOL2 format, chain PA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain NA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain VA [auth C] mmCIF format, chain V [auth B] mmCIF format, chain UA [auth C] mmCIF format, chain U [auth B] mmCIF format, chain TA [auth C] mmCIF format, chain SA [auth C] mmCIF format, chain RA [auth C] mmCIF format, chain QA [auth C] mmCIF format, chain PA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain O [auth A] mmCIF format, chain NA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain FA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] EA [auth B] AA [auth B], BA [auth B], CA [auth B], DA [auth B], EA [auth B], FA [auth B], H [auth A], I [auth A], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], NA [auth C], O [auth A], OA [auth C], P [auth A], PA [auth C], QA [auth C], RA [auth C], SA [auth C], TA [auth C], U [auth B], UA [auth C], V [auth B], VA [auth C], W [auth B], X [auth B], Y [auth B], Z [auth B]	UNKNOWN ATOM OR ION X	👁 Image	Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain U [auth B] Focus chain UA [auth C] Focus chain V [auth B] Focus chain VA [auth C] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain MA [auth C] Focus chain N [auth A] Focus chain NA [auth C] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain PA [auth C] Focus chain QA [auth C] Focus chain RA [auth C] Focus chain SA [auth C] Focus chain TA [auth C] Focus chain U [auth B] Focus chain UA [auth C] Focus chain V [auth B] Focus chain VA [auth C] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.238 (Depositor), 0.240 (DCC)
R-Value Work: 0.199 (Depositor), 0.210 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.159	α = 90
b = 94.159	β = 90
c = 281.894	γ = 120

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2013-07-03

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2013-07-03
Type: Initial release
Version 1.1: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description