OCA Atlas for 4V5C

4V5C

Structure of the Thermus thermophilus 70S ribosome in complex with mRNA, paromomycin, acylated A-site tRNA, deacylated P-site tRNA, and E-site tRNA.

date

authors

Voorhees, R.M., Weixlbaumer, A., Loakes, D., Kelley, A.C., Ramakrishnan, V.

compound

source

symmetry

R_factor

R_Free

0.272

crystal
cell

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

method

X-Ray Diffraction

resolution

3.30

note

4V5C supersedes 2WDG, 2WDH, 2WDI, 2WDJ

Gene
Ontology

Chain	Function	Process	Component
AB, CB
AC, CC
AH, CH
AI, CI
AL, CL
AM, CM
AN, CN
AO, CO
AS, CS
AT, CT
AU, CU
B0, D0
B1, D1
B3, D3
B4, D4
B6, D6
B7, D7
BC, DC
BE, DE
BF, DF
BN, DN
BO, DO
BQ, DQ
BS, DS
BT, DT
BW, DW
BX, DX
BY, DY
CD, AD
CE, AE
CF, AF
CG, AG
CJ, AJ
CK, AK
CP, AP
CQ, AQ
CR, AR
D2, B2
D5, B5
D8, B8
D9, B9
DD, BD
DG, BG
DH, BH
DI, BI
DP, BP
DR, BR
DU, BU
DV, BV
DZ, BZ

Primary reference

Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome., Voorhees RM, Weixlbaumer A, Loakes D, Kelley AC, Ramakrishnan V, Nat Struct Mol Biol. 2009 May;16(5):528-33. Epub 2009 Apr 12. PMID:19363482

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1193 Kb) [Save to disk]

CSU: Contacts of Structural Units for 4V5C

Structure Factors (9238 Kb)

Retrieve 4V5C in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 4V5C from S2C, [Save to disk]

View 4V5C 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 4V5C

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: [4v5c_DP] [4v5c_CS] [4v5c_CA] [4v5c_B3] [4v5c_DF] [4v5c_DH] [4v5c_AH] [4v5c_AI] [4v5c_DS] [4v5c_AV] [4v5c_D2] [4v5c_B9] [4v5c_BO] [4v5c_DA] [4v5c_D6] [4v5c_BH] [4v5c_AG] [4v5c_CG] [4v5c_DC] [4v5c_DT] [4v5c_B0] [4v5c_CF] [4v5c] [4v5c_DB] [4v5c_CI] [4v5c_BQ] [4v5c_BR] [4v5c_DD] [4v5c_DN] [4v5c_AN] [4v5c_CJ] [4v5c_DR] [4v5c_BW] [4v5c_AP] [4v5c_B4] [4v5c_BE] [4v5c_AF] [4v5c_AK] [4v5c_AT] [4v5c_AL] [4v5c_BP] [4v5c_D7] [4v5c_AD] [4v5c_BB] [4v5c_AJ] [4v5c_AE] [4v5c_B5] [4v5c_BS] [4v5c_BZ] [4v5c_CR] [4v5c_CX] [4v5c_B1] [4v5c_CB] [4v5c_DZ] [4v5c_CC] [4v5c_BY] [4v5c_D5] [4v5c_AU] [4v5c_BC] [4v5c_BA] [4v5c_DV] [4v5c_B6] [4v5c_CQ] [4v5c_CN] [4v5c_DO] [4v5c_CE] [4v5c_AY] [4v5c_AB] [4v5c_BI] [4v5c_BT] [4v5c_B2] [4v5c_CL] [4v5c_D0] [4v5c_CP] [4v5c_DI] [4v5c_CW] [4v5c_DU] [4v5c_AR] [4v5c_AQ] [4v5c_DG] [4v5c_DY] [4v5c_AO] [4v5c_CK] [4v5c_D1] [4v5c_DQ] [4v5c_BN] [4v5c_CV] [4v5c_CY] [4v5c_DE] [4v5c_AW] [4v5c_BV] [4v5c_AA] [4v5c_DX] [4v5c_AC] [4v5c_AX] [4v5c_D4] [4v5c_BX] [4v5c_D8] [4v5c_BD] [4v5c_BG] [4v5c_DW] [4v5c_AS] [4v5c_CU] [4v5c_CH] [4v5c_B7] [4v5c_CM] [4v5c_B8] [4v5c_D9] [4v5c_CD] [4v5c_BF] [4v5c_CO] [4v5c_AM] [4v5c_BU] [4v5c_D3] [4v5c_CT]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Domains found in 4V5C: [KH] [KOW] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART

Other resources with information on 4V5C

Community annotation for 4V5C at PDBWiki (http://pdbwiki.org)

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