1KD1	Co-crystal Structure of Spiramycin bound to the 50S Ribosomal Subunit of Haloarcula marismortui	date
authors	Hansen, J.L., Ippolito, J.A., Ban, N., Nissen, P., Moore, P.B., Steitz, T.A.
compound		source
symmetry		R_factor R_Free 0.269
crystal cell	length a length b length c angle alpha angle beta angle gamma
method	X-Ray Diffraction	resolution	3.00
ligand	CD, CL, K, MG, NA, SPR	enzyme
related structures	by homologous chain: 1K8A, 1K9M
Gene Ontology	Chain Function Process Component 1 2 3 4 C D E F G H ribonuclease P activity I J K L M N O P Q R S T U V W X Y Z
Primary reference	The structures of four macrolide antibiotics bound to the large ribosomal subunit., Hansen JL, Ippolito JA, Ban N, Nissen P, Moore PB, Steitz TA, Mol Cell 2002 Jul;10(1):117-28. PMID:12150912

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2000 Kb) [Save to disk] Biological Unit Coordinates (1kd1.pdb1.gz) 1961 Kb LPC: Ligand-Protein Contacts for 1KD1 CSU: Contacts of Structural Units for 1KD1 Likely Quarternary Molecular Structure file(s) for 1KD1 Structure Factors (5209 Kb) Retrieve 1KD1 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1KD1 from S2C, [Save to disk] Re-refined 1kd1 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 1KD1 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 1KD1

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1KD1, from MSDmotif at EBI Structure summary from SCOR (Structural Classification of RNA) Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1kd11_, region 1 [Jmol] [rasmolscript] [script source]     - Domain d1kd12_, region 2 [Jmol] [rasmolscript] [script source]     - Domain d1kd13_, region 3 [Jmol] [rasmolscript] [script source]     - Domain d1kd14_, region 4 [Jmol] [rasmolscript] [script source]     - Domain d1kd1c2, region C:1-90 [Jmol] [rasmolscript] [script source]     - Domain d1kd1c1, region C:91-237 [Jmol] [rasmolscript] [script source]     - Domain d1kd1d_, region D [Jmol] [rasmolscript] [script source]     - Domain d1kd1e_, region E [Jmol] [rasmolscript] [script source]     - Domain d1kd1f_, region F [Jmol] [rasmolscript] [script source]     - Domain d1kd1g1, region G:1-79 [Jmol] [rasmolscript] [script source]     - Domain d1kd1g2, region G:80-172 [Jmol] [rasmolscript] [script source]     - Domain d1kd1h_, region H [Jmol] [rasmolscript] [script source]     - Domain d1kd1i_, region I [Jmol] [rasmolscript] [script source]     - Domain d1kd1j_, region J [Jmol] [rasmolscript] [script source]     - Domain d1kd1k_, region K [Jmol] [rasmolscript] [script source]     - Domain d1kd1l_, region L [Jmol] [rasmolscript] [script source]     - Domain d1kd1m_, region M [Jmol] [rasmolscript] [script source]     - Domain d1kd1n_, region N [Jmol] [rasmolscript] [script source]     - Domain d1kd1o_, region O [Jmol] [rasmolscript] [script source]     - Domain d1kd1p_, region P [Jmol] [rasmolscript] [script source]     - Domain d1kd1q_, region Q [Jmol] [rasmolscript] [script source]     - Domain d1kd1r_, region R [Jmol] [rasmolscript] [script source]     - Domain d1kd1s_, region S [Jmol] [rasmolscript] [script source]     - Domain d1kd1t_, region T [Jmol] [rasmolscript] [script source]     - Domain d1kd1u_, region U [Jmol] [rasmolscript] [script source]     - Domain d1kd1v_, region V [Jmol] [rasmolscript] [script source]     - Domain d1kd1w_, region W [Jmol] [rasmolscript] [script source]     - Domain d1kd1x_, region X [Jmol] [rasmolscript] [script source]     - Domain d1kd1y_, region Y [Jmol] [rasmolscript] [script source]     - Domain d1kd1z_, region Z [Jmol] [rasmolscript] [script source] Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1kd1_I] [1kd1_U] [1kd1_Y] [1kd1_V] [1kd1_X] [1kd1_E] [1kd1_F] [1kd1_O] [1kd1_H] [1kd1_Z] [1kd1_Q] [1kd1_G] [1kd1_W] [1kd1_1] [1kd1_A] [1kd1_B] [1kd1] [1kd1_K] [1kd1_M] [1kd1_R] [1kd1_N] [1kd1_T] [1kd1_P] [1kd1_4] [1kd1_L] [1kd1_C] [1kd1_3] [1kd1_J] [1kd1_S] [1kd1_2] [1kd1_D] SWISS-PROT database: [P60617] [P29198] [P22450] [P60618] [P12737] [P12733] [P14123] [P14119] [P12734] [P10970] [P12732] [P14116] [P10972] [P10971] [P20276] [P14121] [P18138] [P12736] [P60619] [P32410] [P22452] [P20279] [P32411] [P12735] [P14124] [P14135] [P12743] [P15825] Domain organization of [RL10_HALMA] [RL13_HALMA] [RL14_HALMA] [RL15E_HALMA] [RL15_HALMA] [RL18E_HALMA] [RL18_HALMA] [RL19_HALMA] [RL21_HALMA] [RL22_HALMA] [RL23_HALMA] [RL24E_HALMA] [RL24_HALMA] [RL29_HALMA] [RL2_HALMA] [RL30_HALMA] [RL31_HALMA] [RL32_HALMA] [RL37A_HALMA] [RL37_HALMA] [RL39_HALMA] [RL3_HALMA] [RL44_HALMA] [RL4_HALMA] [RL5_HALMA] [RL6_HALMA] [RL7A_HALMA] [RLA0_HALMA] by SWISSPFAM Domains found in 1KD1: [HhH1] [KOW] [Ribosomal_L14] [Ribosomal_L15e] [Ribosomal_L19e] [Ribosomal_L2] [Ribosomal_L2_C] [Ribosomal_L31e] [Ribosomal_L32e] [TRASH ] by SMART

Other resources with information on 1KD1

Community annotation for 1KD1 at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---