5VYC Ribosome date 7-0 20, 1998
authors I.B.Lomakin, E.A.Stolboushkina, A.T.Vaidya, M.B.Garber, S.E. T.A.Steitz
compound source
symmetry Space Group: P 1 21 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
334.670 597.130 336.500 90.00 120.29 90.00
method X-Ray Diffractionresolution
Gene
Ontology
ChainFunctionProcessComponent
A1, A3, A6, A4, A2, A5
  • virus receptor activity

  • cytosolic small ribosomal su...
  • B6, B1, B3, B5, B4, B2

  • cytosolic small ribosomal su...
  • C1, C5, C2, C6, C4, C3

  • cytosolic small ribosomal su...
  • D2, D4, D1, D6, D5, D3

  • cytosolic small ribosomal su...
  • E3, E4, E6, E2, E1, E5

  • ribosome
  • cytosolic small ribosomal su...
  • F3, F6, F5, F2, F1, F4

  • cytosolic small ribosomal su...
  • G6, G2, G4, G1, G3, G5

  • cytosolic small ribosomal su...
  • H3, H6, H1, H2, H4, H5

  • cytosolic small ribosomal su...
  • I5, I1, I3, I6, I4, I2

  • cytosolic small ribosomal su...
  • J2, J6, J5, J1, J3, J4

  • cytosolic small ribosomal su...
  • K3, K6, K1, K4, K2, K5

  • cytosolic small ribosomal su...
  • L1, L2, L6, L4, L5, L3

  • cytosolic small ribosomal su...
  • M1, M3, M5, M2, M4, M6

  • cytosolic small ribosomal su...
  • N2, N6, N4, N3, N5, N1

  • cytosolic small ribosomal su...
  • O4, O1, O3, O5, O2, O6
  • translation regulator activi...

  • cytosolic small ribosomal su...
  • P3, P5, P1, P2, P4, P6

  • cytosolic small ribosomal su...
  • Q3, Q5, Q2, Q6, Q4, Q1

  • cytosolic small ribosomal su...
  • R1, R3, R6, R4, R5, R2

  • cytosolic small ribosomal su...
  • S4, S1, S3, S5, S6, S2

  • small ribosomal subunit
  • cytosolic small ribosomal su...
  • T1, T3, T2, T5, T4, T6

  • cytosolic small ribosomal su...
  • U3, U1, U6, U4, U2, U5

  • cytosolic small ribosomal su...
  • V5, V1, V3, V6, V4, V2

  • cytosolic small ribosomal su...
  • W1, W2, W5, W3, W4, W6

  • cytosolic small ribosomal su...
  • X6, X3, X1, X4, X2, X5

  • cytosolic small ribosomal su...
  • Y6, Y1, Y3, Y2, Y5, Y4

  • small ribosomal subunit
  • cytosolic small ribosomal su...
  • Z3, Z1, Z5, Z2, Z6, Z4

  • small ribosomal subunit
  • cytosolic small ribosomal su...
  • a2, a1, a5, a6, a3, a4

  • small ribosomal subunit
  • cytosolic small ribosomal su...
  • b6, b4, b5, b1, b3, b2

  • cytosolic small ribosomal su...
  • c4, c1, c6, c3, c5, c2

  • small ribosomal subunit
  • cytosolic small ribosomal su...
  • d4, d6, d2, d1, d3, d5

  • small ribosomal subunit
  • cytosolic small ribosomal su...
  • e2, e5, e3, e1, e6, e4


    f4, f2, f1, f3, f5, f6


    g1, g5, g6, g3, g4, g2
  • protein tyrosine kinase inhi...


  • j2, j6, j4, j3, j5, j1


    k5, k2, k1, k3, k4, k6


    l3, l4, l1, l2, l6, l5


    Primary referenceCrystal Structure of the Human Ribosome in Complex with DENR-MCT-1., Lomakin IB, Stolboushkina EA, Vaidya AT, Zhao C, Garber MB, Dmitriev SE, Steitz TA, Cell Rep. 2017 Jul 18;20(3):521-528. doi: 10.1016/j.celrep.2017.06.025. PMID:28723557
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (4171 Kb) [Save to disk]
  • CSU: Contacts of Structural Units for 5VYC
  • Structure Factors (8981 Kb)
  • Retrieve 5VYC in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5VYC from S2C, [Save to disk]
  • View 5VYC 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 5VYC
  • 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 5vyc from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5vyc_F1] [5vyc_N2] [5vyc_M1] [5vyc_j3] [5vyc_i3] [5vyc_a2] [5vyc_l1] [5vyc_f2] [5vyc_d2] [5vyc_l2] [5vyc_k3] [5vyc_L2] [5vyc_T2] [5vyc_F3] [5vyc_V6] [5vyc_Y6] [5vyc_d1] [5vyc_P1] [5vyc_C6] [5vyc_e6] [5vyc_C5] [5vyc_I6] [5vyc_D3] [5vyc_d6] [5vyc_Q3] [5vyc_E1] [5vyc_U3] [5vyc_J4] [5vyc_e4] [5vyc_I2] [5vyc_c4] [5vyc_H4] [5vyc_H5] [5vyc_M5] [5vyc_W4] [5vyc_c3] [5vyc_a5] [5vyc_a4] [5vyc_T4] [5vyc_G3] [5vyc_k2] [5vyc_N3] [5vyc_O5] [5vyc_e1] [5vyc_I4] [5vyc_V2] [5vyc_J3] [5vyc_D6] [5vyc_T6] [5vyc_O4] [5vyc_R4] [5vyc_f1] [5vyc_B5] [5vyc_D5] [5vyc_V1] [5vyc_T3] [5vyc_O1] [5vyc_U2] [5vyc_i1] [5vyc_e3] [5vyc_d3] [5vyc_b3] [5vyc_R2] [5vyc_Y2] [5vyc_D4] [5vyc_V5] [5vyc_B4] [5vyc_P2] [5vyc_Q5] [5vyc_A1] [5vyc_U1] [5vyc_N5] [5vyc_X6] [5vyc_X5] [5vyc_f5] [5vyc_H1] [5vyc_Z3] [5vyc_c6] [5vyc_M3] [5vyc_P4] [5vyc_b6] [5vyc_Y4] [5vyc_S1] [5vyc_G1] [5vyc_Y3] [5vyc_N4] [5vyc_g4] [5vyc_B1] [5vyc_E3] [5vyc_e5] [5vyc_Y5] [5vyc_E5] [5vyc_X4] [5vyc_k6] [5vyc_l6] [5vyc_K6] [5vyc_L5] [5vyc_X2] [5vyc_V4] [5vyc_U5] [5vyc_W3] [5vyc_W6] [5vyc_E2] [5vyc_b1] [5vyc_M2] [5vyc_Q2] [5vyc_O6] [5vyc_T5] [5vyc_D1] [5vyc_A6] [5vyc_H3] [5vyc_F5] [5vyc_G5] [5vyc_I5] [5vyc_B2] [5vyc_E4] [5vyc_N6] [5vyc_H6] [5vyc_M6] [5vyc_S3] [5vyc_H2] [5vyc_i2] [5vyc_a1] [5vyc_Z1] [5vyc_P5] [5vyc_c1] [5vyc_d4] [5vyc_l3] [5vyc_i4] [5vyc_l4] [5vyc_P3] [5vyc_c5] [5vyc_b2] [5vyc_F6] [5vyc_g1] [5vyc_I3] [5vyc_j4] [5vyc_a3] [5vyc_k1] [5vyc_Q1] [5vyc_B6] [5vyc_b4] [5vyc_G2] [5vyc_f6] [5vyc_Z2] [5vyc_O2] [5vyc_N1] [5vyc_F4] [5vyc_k5] [5vyc_L4] [5vyc_j1] [5vyc_j5] [5vyc_K3] [5vyc_S2] [5vyc_Q6] [5vyc_T1] [5vyc_G6] [5vyc_L1] [5vyc_f3] [5vyc_R1] [5vyc_J2] [5vyc_F2] [5vyc_A3] [5vyc_K1] [5vyc_R6] [5vyc_W5] [5vyc_f4] [5vyc_R5] [5vyc_j2] [5vyc_V3] [5vyc_i6] [5vyc_W1] [5vyc_Z6] [5vyc_e2] [5vyc_b5] [5vyc_J6] [5vyc_X1] [5vyc_M4] [5vyc_g6] [5vyc_g5] [5vyc_A4] [5vyc_C3] [5vyc_k4] [5vyc_C1] [5vyc_O3] [5vyc_K4] [5vyc_K5] [5vyc_a6] [5vyc_L6] [5vyc_S6] [5vyc_D2] [5vyc_d5] [5vyc_E6] [5vyc_g2] [5vyc_j6] [5vyc_U4] [5vyc_X3] [5vyc_S5] [5vyc_g3] [5vyc_K2] [5vyc_A5] [5vyc_Q4] [5vyc_J1] [5vyc_l5] [5vyc_P6] [5vyc_C4] [5vyc_i5] [5vyc_Y1] [5vyc_B3] [5vyc_L3] [5vyc_W2] [5vyc_I1] [5vyc_G4] [5vyc_c2] [5vyc_S4] [5vyc_Z4] [5vyc_U6] [5vyc_A2] [5vyc_C2] [5vyc_Z5] [5vyc_J5] [5vyc_R3]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5VYC
  • Community annotation for 5VYC at PDBWiki (http://pdbwiki.org)

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