1NBF Hydrolase date Dec 02, 2002
title Crystal Structure Of A Ubp-Family Deubiquitinating Enzyme In And In Complex With Ubiquitin Aldehyde
authors M.Hu, P.Li, M.Li, W.Li, T.Yao, J.W.Wu, W.Gu, R.E.Cohen, Y.Shi
compound source
Molecule: Ubiquitin Carboxyl-Terminal Hydrolase 7
Chain: A, B, E
Fragment: Hausp Core Domain
Synonym: Deubiquitinating Enzyme 7
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Usp7
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_plasmid: Pgex-2t

Molecule: Ubiquitin Aldehyde
Chain: C, D
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Uba52
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.218 R_Free 0.262
length a length b length c angle alpha angle beta angle gamma
99.728 101.166 141.134 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand GLZ enzyme Hydrolase E.C. BRENDA
related structures by homologous chain: 1AAR, 1NB8, 1TBE
A, E, B

Primary referenceCrystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde., Hu M, Li P, Li M, Li W, Yao T, Wu JW, Gu W, Cohen RE, Shi Y, Cell 2002 Dec 27;111(7):1041-54. PMID:12507430
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (206 Kb) [Save to disk]
  • Biological Unit Coordinates (1nbf.pdb1.gz) 75 Kb
  • Biological Unit Coordinates (1nbf.pdb2.gz) 74 Kb
  • Biological Unit Coordinates (1nbf.pdb3.gz) 59 Kb
  • LPC: Ligand-Protein Contacts for 1NBF
  • CSU: Contacts of Structural Units for 1NBF
  • Likely Quarternary Molecular Structure file(s) for 1NBF
  • Retrieve 1NBF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1NBF from S2C, [Save to disk]
  • View 1NBF in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 1NBF
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1NBF, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1nbfa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1nbfb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1nbfc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1nbfd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1nbfe_, region E [Jmol] [rasmolscript] [script source]
  • Fold representative 1nbf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1nbf_D] [1nbf_C] [1nbf_B] [1nbf_A] [1nbf_E] [1nbf]
  • SWISS-PROT database: [P62988] [Q93009]
  • Domain organization of [UBIQ_HUMAN] [UBP7_HUMAN] by SWISSPFAM
  • Domain found in 1NBF: [UBQ ] by SMART
  • Other resources with information on 1NBF
  • Community annotation for 1NBF at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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