OCA Atlas for 4V5S

4V5S

The crystal structure of EF-Tu and G24A-tRNA-Trp bound to a cognate codon on the 70S ribosome.

date

authors

Schmeing, T.M., Voorhees, R.M., Ramakrishnan, V.

compound

source

symmetry

R_factor

R_Free

0.2846

crystal
cell

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

method

X-Ray Diffraction

resolution

3.10

note

4V5S supersedes 2Y14, 2Y15, 2Y16, 2Y17

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
CZ, AZ
D2, B2
D5, B5
D8, B8
D9, B9
DD, BD
DG, BG
DH, BH
DP, BP
DR, BR
DU, BU
DV, BV
DZ, BZ

Primary reference

How mutations in tRNA distant from the anticodon affect the fidelity of decoding., Schmeing TM, Voorhees RM, Kelley AC, Ramakrishnan V, Nat Struct Mol Biol. 2011 Apr;18(4):432-6. Epub 2011 Mar 6. PMID:21378964

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1276 Kb) [Save to disk]

CSU: Contacts of Structural Units for 4V5S

Structure Factors (9291 Kb)

Retrieve 4V5S in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 4V5S from S2C, [Save to disk]

View 4V5S 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 4V5S

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: [4v5s_CF] [4v5s_CQ] [4v5s_AM] [4v5s_AN] [4v5s_BU] [4v5s_AB] [4v5s_BX] [4v5s_AP] [4v5s_CA] [4v5s_AI] [4v5s_DR] [4v5s_B4] [4v5s_BW] [4v5s_DB] [4v5s_D6] [4v5s_CO] [4v5s_BJ] [4v5s_BV] [4v5s_AH] [4v5s_AZ] [4v5s_CD] [4v5s_B8] [4v5s_CB] [4v5s_DU] [4v5s_BF] [4v5s_BG] [4v5s_AD] [4v5s_DC] [4v5s_D0] [4v5s_BO] [4v5s_DF] [4v5s_CL] [4v5s_DS] [4v5s_BE] [4v5s_DT] [4v5s_AT] [4v5s_CJ] [4v5s_CZ] [4v5s_D4] [4v5s_CY] [4v5s_AX] [4v5s_CC] [4v5s_CW] [4v5s_D1] [4v5s_BK] [4v5s_AR] [4v5s_AQ] [4v5s_AV] [4v5s_CH] [4v5s_AG] [4v5s_AK] [4v5s] [4v5s_AU] [4v5s_D2] [4v5s_BN] [4v5s_DH] [4v5s_DA] [4v5s_BY] [4v5s_B5] [4v5s_B9] [4v5s_AC] [4v5s_DV] [4v5s_BB] [4v5s_B3] [4v5s_DG] [4v5s_CP] [4v5s_DP] [4v5s_DX] [4v5s_D7] [4v5s_CX] [4v5s_AO] [4v5s_B1] [4v5s_CS] [4v5s_CN] [4v5s_AJ] [4v5s_AE] [4v5s_AL] [4v5s_CM] [4v5s_D5] [4v5s_DO] [4v5s_AF] [4v5s_DW] [4v5s_DY] [4v5s_B0] [4v5s_CR] [4v5s_DK] [4v5s_BD] [4v5s_BC] [4v5s_DN] [4v5s_BT] [4v5s_DZ] [4v5s_BA] [4v5s_BQ] [4v5s_CT] [4v5s_DQ] [4v5s_BP] [4v5s_D3] [4v5s_DJ] [4v5s_CK] [4v5s_AY] [4v5s_B2] [4v5s_AS] [4v5s_B7] [4v5s_BR] [4v5s_AW] [4v5s_D8] [4v5s_BZ] [4v5s_CV] [4v5s_BS] [4v5s_B6] [4v5s_DD] [4v5s_CE] [4v5s_BH] [4v5s_CG] [4v5s_CU] [4v5s_AA] [4v5s_D9] [4v5s_CI] [4v5s_DE]

SWISS-PROT database:

Domain organization of by SWISSPFAM

Domains found in 4V5S: [KH] [KOW] [Ribosomal_L14] [Ribosomal_L2] [Ribosomal_L2_C] [Ribosomal_S10] [Ribosomal_S15] [Ribosomal_S4] [S4 ] by SMART

Other resources with information on 4V5S

Community annotation for 4V5S at PDBWiki (http://pdbwiki.org)

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