OCA Atlas for 6YPU

6YPU

date

authors

compound

source

symmetry

R_factor

R_Free

crystal
cell

length a	length b	length c	angle alpha	angle beta	angle gamma

method

X-Ray Diffraction

resolution

ligand

AKN, MG

enzyme

Gene
Ontology

Chain	Function	Process	Component
c
e
f
g
i
l
m
p
q
r
s
u
v

Primary reference

Structure of the 70S Ribosome from the Human Pathogen Acinetobacter baumannii in Complex with Clinically Relevant Antibiotics., Nicholson D, Edwards TA, O'Neill AJ, Ranson NA, Structure. 2020 Aug 26. pii: S0969-2126(20)30286-0. doi:, 10.1016/j.str.2020.08.004. PMID:32857965

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (586 Kb) [Save to disk]

Biological Unit Coordinates (6ypu.pdb1.gz) 571 Kb

LPC: Ligand-Protein Contacts for 6YPU

CSU: Contacts of Structural Units for 6YPU

Retrieve 6YPU in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 6YPU from S2C, [Save to disk]

View 6YPU 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 6YPU

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

Fold representative 6ypu from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [6ypu_2] [6ypu_4] [6ypu_c] [6ypu_e] [6ypu_f] [6ypu_g] [6ypu_i] [6ypu_l] [6ypu_m] [6ypu_p] [6ypu_q] [6ypu_r] [6ypu_s] [6ypu_u] [6ypu_v]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Other resources with information on 6YPU

Community annotation for 6YPU at PDBWiki (http://pdbwiki.org)

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