OCA Atlas for 5D4C

5D4C

date

authors

compound

source

symmetry

R_factor

R_Free

crystal
cell

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

method

X-Ray Diffraction

resolution

ligand

ATP, C, C5P, CTP, MG, ZN

enzyme

Gene
Ontology

Chain	Function	Process	Component
B, L, K, A
D, N
E, O
F, P	bacterial sigma factor activ...
M, C

Primary reference

The mechanism of RNA 5' capping with NAD+, NADH and desphospho-CoA., Bird JG, Zhang Y, Tian Y, Panova N, Barvik I, Greene L, Liu M, Buckley B, Krasny L, Lee JK, Kaplan CD, Ebright RH, Nickels BE, Nature. 2016 Jul 21;535(7612):444-7. PMID:27383794

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1142 Kb) [Save to disk]

Biological Unit Coordinates (5d4c.pdb1.gz) 576 Kb

Biological Unit Coordinates (5d4c.pdb2.gz) 571 Kb

LPC: Ligand-Protein Contacts for 5D4C

CSU: Contacts of Structural Units for 5D4C

Structure Factors (1450 Kb)

Retrieve 5D4C in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 5D4C from S2C, [Save to disk]

Re-refined 5d4c structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5D4C 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.

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: [5d4c] [5d4c_A] [5d4c_B] [5d4c_C] [5d4c_D] [5d4c_E] [5d4c_F] [5d4c_G] [5d4c_H] [5d4c_K] [5d4c_L] [5d4c_M] [5d4c_N] [5d4c_O] [5d4c_P] [5d4c_R] [5d4c_S]

SWISS-PROT database:

Domains found in 5D4C: [HhH1] [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART

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