1. General information
Table1. General information of 4OOG
| General information |
|
PDB_ID
|
PubMed
|
RNA class
|
RNA chain
|
RNA Nts
|
Protein chains
|
Protein length
|
Method
|
Re(Å)[1]
|
Description
|
| 4OOG |
24703949 |
dsRNA |
D |
34 |
A,B,C |
110,110,261 |
X-RAY DIFFRACTION |
2.5 |
Crystal structure of yeast RNase III (Rnt1p) complexed with the product of dsRNA processing. |
2. Pocket information of 4OOG
Table2. Pocket information of RNA chain
| Pocket information |
|
R_P_ID[2]
|
V(Å3)[3]
|
A(Å2)[4]
|
Rc (Å)[5]
|
R(Å)[6]
|
ψ[7]
|
| r_4OOG_0 |
2286 |
1236 |
(-35.8, -22.4, -24.0) |
5.55 |
0.68 |
Table3. Pocket information of protein chains
| Pocket information |
|
Protein chain
|
P_P_ID[8]
|
V(Å3)
|
A(Å2)
|
Rc (Å)
|
R(Å)[9]
|
D(Å)[10]
|
enclose[11]
|
c⁄a[12]
|
b⁄a[13]
|
D S[14]
|
| chain A |
p_4OOG_0 |
794.43 |
782.64 |
(36.49, -73.86, 39.12) |
21.83 |
34.58 |
0.29 |
0.04 |
0.14 |
0.87 |
| p_4OOG_1 |
380.67 |
312.52 |
(53.81, -63.41, 35.31) |
11.06 |
11.54 |
0.28 |
0.14 |
0.34 |
0.58 |
| p_4OOG_2 |
153.34 |
199.55 |
(64.31, -64.91, 33.93) |
6.61 |
9.93 |
0.12 |
0.33 |
0.62 |
0.31 |
| p_4OOG_3 |
107.01 |
419.09 |
(52.67, -79.15, 40.29) |
9.09 |
9.16 |
0.33 |
0.10 |
0.27 |
0.23 |
| chain B |
p_4OOG_0 |
909.63 |
730.82 |
(53.13, -62.45, 26.23) |
19.90 |
27.90 |
0.30 |
0.06 |
0.28 |
0.84 |
| p_4OOG_1 |
338.43 |
294.93 |
(37.00, -72.56, 28.84) |
9.82 |
13.98 |
0.26 |
0.16 |
0.36 |
0.63 |
| p_4OOG_2 |
194.62 |
206.29 |
(31.68, -72.81, 39.44) |
7.46 |
10.92 |
0.39 |
0.11 |
0.12 |
0.39 |
| p_4OOG_3 |
132.86 |
145.64 |
(33.50, -82.09, 28.67) |
6.61 |
7.95 |
0.14 |
0.29 |
0.43 |
0.22 |
| chain C |
p_4OOG_0 |
307.16 |
417.28 |
(-9.88, -57.86, -0.62) |
11.76 |
17.02 |
0.20 |
0.09 |
0.14 |
0.70 |
| p_4OOG_1 |
275.95 |
275.95 |
(34.43, -55.65, 13.74) |
12.36 |
14.43 |
0.27 |
0.07 |
0.55 |
0.57 |
| p_4OOG_2 |
232.86 |
649.14 |
(12.95, -74.45, 0.60) |
10.84 |
13.78 |
0.18 |
0.07 |
0.13 |
0.56 |
| p_4OOG_3 |
218.25 |
462.43 |
(22.68, -65.66, 14.52) |
7.92 |
10.11 |
0.22 |
0.16 |
0.25 |
0.36 |
| p_4OOG_4 |
211.11 |
526.15 |
(-9.64, -74.09, -6.49) |
9.53 |
12.69 |
0.23 |
0.08 |
0.13 |
0.50 |
| p_4OOG_5 |
201.90 |
459.22 |
(-9.92, -61.13, -12.15) |
8.68 |
9.28 |
0.22 |
0.10 |
0.14 |
0.31 |
| p_4OOG_6 |
200.65 |
479.43 |
(47.47, -41.60, 32.08) |
7.96 |
7.57 |
0.22 |
0.20 |
0.31 |
0.28 |
| p_4OOG_7 |
189.53 |
450.13 |
(-15.06, -70.12, 8.25) |
8.22 |
12.59 |
0.13 |
0.16 |
0.27 |
0.47 |
| p_4OOG_8 |
186.54 |
495.26 |
(6.00, -75.91, 11.29) |
10.95 |
10.60 |
0.14 |
0.06 |
0.13 |
0.40 |
| p_4OOG_9 |
186.29 |
313.95 |
(36.28, -42.46, 25.83) |
8.38 |
10.79 |
0.17 |
0.15 |
0.19 |
0.38 |
| p_4OOG_10 |
182.05 |
446.09 |
(2.91, -80.65, -1.09) |
8.34 |
9.21 |
0.21 |
0.19 |
0.48 |
0.33 |
| p_4OOG_11 |
178.57 |
309.17 |
(15.93, -52.75, 9.28) |
8.69 |
10.34 |
0.43 |
0.15 |
0.18 |
0.38 |
| p_4OOG_12 |
119.04 |
208.62 |
(44.42, -34.43, 21.98) |
6.10 |
6.31 |
0.26 |
0.24 |
0.48 |
0.15 |
Note. [1] Re: resolution of the structure; [2]R_P_ID: RNA pocket ID; [3] V: volume of the pocket; [4] A: surface area of the pocket; [5] Rc: center of mass of the pocket; [6] R: effective radius of the pocket; [7] ψ: a measure of how much the pocket resembles a sphere; [8] P_P_ID: protein pocket ID. [9] R: maximum radius of the pocket;[10] D: depth of the pocket.[11] enclose: ratio of number of surface to hull grid points;[12] c⁄a: ellipsoid main axes ratios, with a > b > c;[13] b⁄a: ellipsoid main axes ratios, with a>b>c;[14] D S : DrugScore for protein pocket