wwPDB validation report of PDB entry 3DU7

the same complex but without the phomopsin A ligand

the same complex but with vinblastine instead of phomopsin A

THERE IS ONE COMPLEX IN THE ASYMMETRIC UNIT, WHICH CONSISTS OF TWO ALPHA-BETA TUBULIN HETERODIMERS (CHAINS A-B AND C-D), AND ONE STATHMIN-LIKE DOMAIN OF RB3 (RB3-SLD) WHICH CORRESPONDS TO STAHMIN RESIDUES 5 TO 145 WITH THE ADDITION OF ONE ACETYLATED ALANINE AT THE N-TERMINUS. THE NUMBERING OF RB3-SLD IS ACCORDING TO THE STATHMIN SEQUENCE. ALPHA- TUBULIN AND BETA-TUBULIN HAVE BEEN ALIGNED AS IN NOGALES ET AL., NATURE VOL 391,199-203. IN THIS ALIGNMENT, RESIDUES 45-46 AND 361-368 OF ALPHA-TUBULIN ARE MISSING IN BETA- TUBULIN. THERE ARE SEVERAL EXPRESSED TUBULIN ISOTYPES IN MAMMALIAN BRAIN. WE USED THE BOS TAURUS TUBULIN SEQUENCE OF THE MOST ABUNDANT ISOTYPES (ALPHA: ISOTYPE 1, GI:73586894, BETA: ISOTYPE 2, GI:51491829) BUT WITH THE ILE TO VAL SUBSTITUTION AT POSITION 318 ON BETA TUBULIN.

Care should be exercised in interpreting the current model due to the limited (4.1 angstroms) resolution.

Tubulin alpha-1C chain, Tubulin beta-2B chain, Stathmin-4
Tubulin-colchicine-phomopsin A: Stathmin-like domain complex

The largest off-origin peak in the Patterson function is 1.95% of the height of the origin peak. No significant pseudotranslation is detected.

structure factor analysis and validation
geometric validation package for ligand chemistry in protein x-ray structures
20191225.v01 (using entries in the PDB archive December 25th 2019)