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. Author manuscript; available in PMC: 2011 Jul 13.
Published in final edited form as: Biochemistry. 2010 Jul 13;49(27):5683–5704. doi: 10.1021/bi100110x

Table 1.

Pairs of protein structures, DDMs, their characteristics and types of movements.

Pair # Pair PDB Resid. includ Biomol d Unit cell e RMSDD Å Δ % δ % Max move Rigid motions RMSDD / Δ final (Å / %) Type
1 1cll1ctr 138c m 12.83 54.92 4.08 46.7 5 0.44 / 2.70 tweezers
2 4cd21cd2 202 m 1.25 2.62 11.7 11 0.44 / 4.74 tweezers
3 4ake1ank 214 m 2 6.45 59.62 16.75 24.8 >12 glove/tweezers
4 1akz1ssp 223 m/tr 1.14 21.89 3.19 5.5 11 0.31 / 0.61 tweezers
4’ 7 0.45 / 4.07
5 2tbv2tbva 287 v. shell 3 1.37 32.22 2.67 6.5 3 0.27 / 1.11 hinge
5’ 2 0.43 / 3.35
6 1l3f3tmn 316 m/tetr 0.46 3.35 0.38 1.8 2 0.36 / 0.69 pliers
7 4ape5er2 330 m/d 0.45 5.21 0.54 2.7 2 0.40 / 2.47 pliers
8 6ldh1ldm 329b tetr 1.25 15.37 4.53 12.3 10 0.41 / 2.86 tweezers
8’ 7 0.45 / 4.14
8”g 8 0.43 / 3.70
9 2gd11gd1 334 tetr 0.49 6.14 0.74 3.1 2 0.36 / 1.89 pliers
10 1erk2erk 353 m 2.24 27.88 3.81 13.8f >12 glove/tweezers
11 8adh6adh 374b d 1/2 1.05 21.90 2.89 5.7 12 0.45 / 2.61 tweezers
12 9aat1ama 401 d 2/1 1.20 22.96 7.48 6.7 7 0.36 / 2.52 tweezers
12’ 3 0.43 / 4.12
13 16pk13pk 415b m/d 1/4 3.07 45.61 4.39 13.3 >12 glove/tweezers
14 1v4t1v4s 424 m 6.90 49.24 5.66 38.9 >12 glove/tweezers
15 4cts1cts 437 d 2 1.58 26.30 12.20 9.6 >12 glove/tweezers
16 1hrd1bgv 449 h 4 1.89 32.85 1.15 8.5 5 0.22 / 0.01 pliers
16’ 2 0.35 / 1.84
17 1lfh1lfg 691b m 4.77 41.43 1.51 24.9 11 0.37 / 2.00 tweezers
17’ 7 0.45 / 3.19
a

there are 3 molecules in the 2tbv unit cell; 2 of them (A and B) do not have 102 residues or Cα atoms on the N-terminus; the 3rd (C) molecule is missing only 66 residues; we used A and C (shortened) molecules with the same number of resolved residues in the calculation.

b

for #13 3 N-terminal and 2 C-terminal residues, which dramatically change their conformation, were not included in the fitting and RMSDD evaluation; such non-included residues can be denoted by -3N, -2C for #13 and similarly indicate non-included residues in other structures; #17: -4N, -1C; #17’: -4N, -7C; #8 -5C; #11: -4N;

c

to make molecules comparable residues 1-3 and 148, missing in 1cll, and residues 76-80, missing in 1ctr, are not included in the DDM comparison.

d

likely but not fully reliable oligomerization state of biologically active molecule, estimates from PQS; notations in the table: m=monomeric, d=dimeric, tr=trimeric, tetr=tetrameric, h=hexameric.

e

number of molecules in the crystallographic unit cell; not shown – means 1; 1/2 means that 1st PDB entry (e.g., 8adh) has 1 molecule in the unit cell, and the second (e.g., 6adh) has 2 molecules in the unit cell.

f

9 N-terminal and 3 C-terminal residues move very far in a non-rigid manner; the value is given for the maximum DD closer to the middle of the chain.

g

characteristics of the transformation identical to 8’ except dividing 96-104 into 96-100 and 101-104 rigid fragments.