OCA Atlas for 5D4D

5D4D

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

A, AMP, C, C5P, CTP, MG, NAD, ZN

enzyme

Gene

Gene
Ontology

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

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] (1151 Kb) [Save to disk]

Biological Unit Coordinates (5d4d.pdb1.gz) 582 Kb

Biological Unit Coordinates (5d4d.pdb2.gz) 573 Kb

LPC: Ligand-Protein Contacts for 5D4D

CSU: Contacts of Structural Units for 5D4D

Structure Factors (1982 Kb)

Retrieve 5D4D in mmCIF format [Save to disk]

SEQRES to COORDINATES correlation for 5D4D from S2C, [Save to disk]

Re-refined 5d4d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5D4D 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: [5d4d] [5d4d_A] [5d4d_B] [5d4d_C] [5d4d_D] [5d4d_E] [5d4d_F] [5d4d_G] [5d4d_H] [5d4d_K] [5d4d_L] [5d4d_M] [5d4d_N] [5d4d_O] [5d4d_P] [5d4d_R] [5d4d_S]

SWISS-PROT database:

Domains found in 5D4D: [HhH1] [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART

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