OCA Atlas for 4V87

4V87

Crystal structure analysis of ribosomal decoding.

date

authors

Demeshkina, N., Jenner, L., Yusupov, M., Yusupova, G.

compound

source

symmetry

R_factor

R_Free

0.2399

crystal
cell

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

method

X-Ray Diffraction

resolution

3.10

note

4V87 supersedes 3TVE, 3TVF, 3TVG, 3TVH

Gene
Ontology

Chain	Function	Process	Component
A1, D1
A2, D2
A3, D3
AE, DE
AF, DF
AM, DM
AN, DN
AO, DO
AS, DS
AT, DT
AW, DW
AX, DX
AZ, DZ
BF, CF
BI, CI
BL, CL
BN, CN
BO, CO
BQ, CQ
BS, CS
BW, CW
BX, CX
CE, BE
CG, BG
CH, BH
CJ, BJ
CK, BK
CM, BM
CP, BP
CR, BR
CT, BT
CU, BU
CV, BV
D0, A0
D4, A4
D5, A5
D6, A6
D7, A7
D8, A8
DD, AD
DG, AG
DH, AH
DK, AK
DP, AP
DQ, AQ
DR, AR
DU, AU
DV, AV

Primary reference

A new understanding of the decoding principle on the ribosome., Demeshkina N, Jenner L, Westhof E, Yusupov M, Yusupova G, Nature. 2012 Mar 21. doi: 10.1038/nature10913. PMID:22437501

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1843 Kb) [Save to disk]

CSU: Contacts of Structural Units for 4V87

Structure Factors (10040 Kb)

Retrieve 4V87 in mmCIF format [Save to disk]

View 4V87 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 4V87

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [4v87_BI] [4v87_CA] [4v87_BP] [4v87_BS] [4v87_A0] [4v87_BR] [4v87_BN] [4v87_AO] [4v87_AH] [4v87_DQ] [4v87_AK] [4v87_A8] [4v87_BA] [4v87_A2] [4v87_CJ] [4v87_AD] [4v87_AP] [4v87_CL] [4v87_AV] [4v87_DN] [4v87_AA] [4v87_BE] [4v87_CQ] [4v87_AE] [4v87_D2] [4v87_BU] [4v87_CM] [4v87_BW] [4v87_DU] [4v87_DH] [4v87_BK] [4v87_CF] [4v87_BL] [4v87_DO] [4v87_CO] [4v87_BQ] [4v87_DS] [4v87_CT] [4v87_A4] [4v87_CK] [4v87_CN] [4v87_CV] [4v87_D4] [4v87_DR] [4v87_BO] [4v87_D7] [4v87_D3] [4v87_CB] [4v87_DA] [4v87_AB] [4v87_BF] [4v87_A7] [4v87_D8] [4v87_CU] [4v87_CH] [4v87_CD] [4v87_C1] [4v87_CI] [4v87_AQ] [4v87_CC] [4v87_AW] [4v87_DV] [4v87_AS] [4v87] [4v87_CE] [4v87_D5] [4v87_AR] [4v87_D0] [4v87_BD] [4v87_AM] [4v87_A1] [4v87_A3] [4v87_BV] [4v87_DW] [4v87_BJ] [4v87_A5] [4v87_DD] [4v87_AT] [4v87_AZ] [4v87_AX] [4v87_CX] [4v87_D1] [4v87_BB] [4v87_D6] [4v87_DE] [4v87_DK] [4v87_A6] [4v87_DG] [4v87_CW] [4v87_DZ] [4v87_BT] [4v87_AU] [4v87_CG] [4v87_CS] [4v87_DT] [4v87_CR] [4v87_BC] [4v87_BX] [4v87_BH] [4v87_DB] [4v87_DX] [4v87_BG] [4v87_CP] [4v87_AG] [4v87_BM] [4v87_AF] [4v87_AN] [4v87_DF] [4v87_B1] [4v87_DP] [4v87_DM]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Domains found in 4V87: [KH] [KOW] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART

Other resources with information on 4V87

Community annotation for 4V87 at PDBWiki (http://pdbwiki.org)

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