RNAprotDB

All interfaces > All interologs > Interface groups > group140 > 6CBD_A_B,C

Interface analysis

mouse controls

Style

Protein

Cartoon
Licorice
Surface

RNA

Cartoon
Licorice
Surface

Color

Chain
Chain (with hetatm)
Chainbow
Hydrophobicity
Electrostatics (surface only)
Conservation*

View

Focus on

Interface
RNA
Protein
All

Show chains

Interface

show as licorice
show Accessibility
Rim - Core

Contacts -

6CBD_A
6CBD_B,C
Distance
Base Pair
Hbond nuc:res
Base Stacking
Residue conservation
A:65 [LYS] B:16 [U] 2.2 sugar:SC 4.76
A:65 [LYS] B:17 [C] 3.64 4.76
A:66 [CYS] B:17 [C] 3.84 1.03
A:67 [PRO] B:16 [U] 3.85 58.91
A:67 [PRO] B:17 [C] 3.38 58.91
A:68 [ARG] B:13 [A] 4.72 49.62
A:68 [ARG] B:14 [A] 2.38 49.62
A:68 [ARG] B:15 [G] 3.02 49.62
A:68 [ARG] B:16 [U] 4.32 49.62
A:70 [VAL] B:17 [C] 3.92 35.98
A:97 [ARG] B:13 [A] 4.91 60.02
A:97 [ARG] B:14 [A] 3.23 60.02
A:97 [ARG] B:15 [G] 4.46 60.02
A:176 [PRO] B:14 [A] 4.09 29.49
A:176 [PRO] B:15 [G] 4.54 29.49
A:177 [VAL] B:14 [A] 3.83 70.56
A:178 [GLY] B:13 [A] 3.98 78.26
A:178 [GLY] B:14 [A] 3.06 sugar:BB 78.26
A:179 [ARG] B:12 [C] 3.18 base:SC 80.6
A:179 [ARG] B:13 [A] 3.54 80.6
A:220 [SER] B:8 [U] 4.81 C:23 [A] 79.4
A:221 [ALA] B:8 [U] 4.79 C:23 [A] 60.72
A:280 [ARG] B:16 [U] 4.78 57.06
A:280 [ARG] B:17 [C] 3.89 57.06
A:294 [PHE] B:21 [U] 3.41 base/AA stacks 88.74
A:295 [PRO] B:21 [U] 4.78 30.95
A:296 [LEU] B:21 [U] 4.3 0.16
A:308 [VAL] B:21 [U] 4.36 95.69
A:311 [TYR] B:21 [U] 3.51 91.7
A:312 [PHE] B:21 [U] 3.74 90.35
A:316 [HIS] B:21 [U] 4.82 80.94
A:337 [THR] B:21 [U] 3.26 43.31
A:338 [TYR] B:21 [U] 2.57 sugar:BB 57.09
A:339 [LEU] B:21 [U] 4.53 54.75
A:351 [ARG] B:9 [G] 4.13 C:22 [C] 71.47
A:357 [THR] C:24 [A] 4.22 B:7 [U] 67.81
A:358 [ASP] C:24 [A] 2.91 B:7 [U] 50.93
A:358 [ASP] C:25 [U] 3.32 B:6 [A] 50.93
A:361 [THR] C:24 [A] 3.33 B:7 [U] sugar:SC 74.64
A:361 [THR] C:25 [U] 3.19 B:6 [A] 74.64
A:362 [SER] C:25 [U] 3.42 B:6 [A] 70.34
A:362 [SER] C:26 [G] 3.56 B:5 [C] 70.34
A:364 [MET] B:7 [U] 4.98 C:24 [A] 80.85
A:365 [ILE] B:6 [A] 4.98 C:25 [U] 84.1
A:365 [ILE] B:7 [U] 3.36 C:24 [A] 84.1
A:365 [ILE] C:25 [U] 3.58 B:6 [A] 84.1
A:365 [ILE] C:26 [G] 4.2 B:5 [C] 84.1
A:366 [ARG] C:26 [G] 3.85 B:5 [C] 72.81
A:366 [ARG] C:27 [U] 4.17 B:4 [A] 72.81
A:368 [THR] B:7 [U] 3.17 C:24 [A] sugar:SC 78.88
A:375 [ARG] B:7 [U] 4.05 C:24 [A] 95.54
A:434 [VAL] C:30 [A] 3.89 52.36
A:435 [TRP] C:30 [A] 4.44 89.37
A:436 [ASP] C:30 [A] 4.53 85.46
A:437 [MET] C:30 [A] 4.24 67.59
A:438 [ARG] C:30 [A] 3.23 base/AA stacks 60.01
A:438 [ARG] C:31 [A] 4.75 60.01
A:477 [ILE] C:30 [A] 4.31 41.28
A:522 [LEU] B:1 [U] 3.53 75.95
A:524 [GLY] B:1 [U] 2.85 base:BB 29.54
A:525 [LYS] B:1 [U] 3.49 40.09
A:525 [LYS] C:23 [A] 3.43 B:8 [U] 40.09
A:525 [LYS] C:24 [A] 2.99 B:7 [U] 40.09
A:526 [THR] B:1 [U] 3.05 base:BB 46.41
A:529 [TYR] B:1 [U] 2.6 base/AA stacks 90.69
A:533 [LYS] B:1 [U] 2.63 99.0
A:544 [THR] B:1 [U] 3.83 94.4
A:545 [GLN] B:1 [U] 2.85 98.84
A:545 [GLN] B:2 [U] 4.65 C:29 [A] 98.84
A:546 [CYS] B:1 [U] 3.01 86.33
A:546 [CYS] B:2 [U] 4.09 C:29 [A] 86.33
A:547 [VAL] B:1 [U] 3.85 79.97
A:547 [VAL] B:2 [U] 3.73 C:29 [A] 79.97
A:548 [GLN] B:1 [U] 3.13 sugar:SC 46.84
A:548 [GLN] B:2 [U] 2.98 C:29 [A] 46.84
A:551 [ASN] B:1 [U] 4.89 77.94
A:551 [ASN] B:2 [U] 2.62 C:29 [A] 77.94
A:557 [PRO] C:30 [A] 3.93 20.34
A:558 [GLN] B:2 [U] 4.45 C:29 [A] 73.23
A:558 [GLN] C:29 [A] 2.77 B:2 [U] sugar:SC base/AA stacks 73.23
A:558 [GLN] C:30 [A] 3.55 73.23
A:559 [THR] B:2 [U] 3.4 C:29 [A] 68.24
A:559 [THR] C:29 [A] 4.46 B:2 [U] 68.24
A:561 [SER] C:30 [A] 3.05 base:SC 71.02
A:562 [ASN] B:2 [U] 2.9 C:29 [A] base:SC 98.92
A:562 [ASN] B:3 [C] 3.97 C:28 [G] 98.92
A:562 [ASN] C:29 [A] 3.7 B:2 [U] 98.92
A:563 [LEU] B:2 [U] 3.61 C:29 [A] 81.24
A:566 [LYS] B:1 [U] 2.84 98.68
A:566 [LYS] B:2 [U] 3.25 C:29 [A] 98.68
A:566 [LYS] B:3 [C] 2.86 C:28 [G] 98.68
A:570 [LYS] B:1 [U] 3.15 98.79
A:598 [VAL] B:10 [C] 3.83 95.11
A:599 [THR] B:10 [C] 3.48 83.17
A:600 [HIS] B:10 [C] 2.94 base:BB 97.99
A:600 [HIS] B:11 [C] 3.09 sugar:SC 97.99
A:601 [PRO] B:10 [C] 3.38 82.3
A:601 [PRO] B:11 [C] 4.83 82.3
A:602 [PRO] B:9 [G] 3.5 C:22 [C] 67.41
A:602 [PRO] B:10 [C] 4.21 67.41
A:603 [ALA] B:9 [G] 3.06 C:22 [C] sugar:BB 66.41
A:603 [ALA] B:10 [C] 3.46 66.41
A:635 [ARG] B:10 [C] 3.68 78.3
A:635 [ARG] B:11 [C] 2.73 78.3
A:637 [GLU] B:11 [C] 3.02 sugar:SC 95.59
A:670 [GLY] B:11 [C] 4.0 98.63
A:671 [VAL] B:11 [C] 4.26 96.91
A:672 [SER] B:11 [C] 2.93 base:BB, base:SC 95.77
A:672 [SER] B:12 [C] 3.26 95.77
A:674 [GLY] B:12 [C] 3.79 88.42
A:675 [GLN] B:11 [C] 2.73 sugar:SC 91.7
A:675 [GLN] B:12 [C] 3.33 91.7
A:709 [LYS] B:5 [C] 4.78 C:26 [G] 99.0
A:709 [LYS] B:6 [A] 2.71 C:25 [U] 99.0
A:710 [ARG] B:8 [U] 3.33 C:23 [A] 95.16
A:710 [ARG] B:9 [G] 2.66 C:22 [C] base:SC, base:SC 95.16
A:710 [ARG] B:10 [C] 3.47 95.16
A:710 [ARG] C:22 [C] 4.5 B:9 [G] 95.16
A:714 [ARG] B:6 [A] 4.56 C:25 [U] 98.26
A:714 [ARG] B:7 [U] 2.72 C:24 [A] 98.26
A:726 [LYS] C:27 [U] 4.92 B:4 [A] 76.75
A:726 [LYS] C:28 [G] 4.86 B:3 [C] 76.75
A:753 [HIS] B:5 [C] 3.16 C:26 [G] 93.26
A:753 [HIS] B:6 [A] 2.98 C:25 [U] 93.26
A:754 [ALA] B:5 [C] 3.95 C:26 [G] 66.17
A:755 [GLY] B:5 [C] 4.04 C:26 [G] 82.53
A:756 [ILE] B:4 [A] 3.33 C:27 [U] 78.75
A:756 [ILE] B:5 [C] 3.38 C:26 [G] sugar:BB 78.75
A:756 [ILE] C:27 [U] 4.62 B:4 [A] 78.75
A:756 [ILE] C:28 [G] 4.67 B:3 [C] 78.75
A:757 [GLN] B:5 [C] 3.28 C:26 [G] sugar:BB 82.05
A:757 [GLN] B:6 [A] 3.06 C:25 [U] 82.05
A:757 [GLN] C:26 [G] 3.02 B:5 [C] 82.05
A:757 [GLN] C:27 [U] 2.39 B:4 [A] sugar:SC 82.05
A:758 [GLY] B:6 [A] 4.29 C:25 [U] 98.6
A:759 [THR] B:6 [A] 3.46 C:25 [U] 99.0
A:759 [THR] B:7 [U] 4.03 C:24 [A] 99.0
A:760 [SER] B:5 [C] 4.95 C:26 [G] 92.15
A:760 [SER] B:6 [A] 3.51 C:25 [U] 92.15
A:761 [ARG] B:6 [A] 2.78 C:25 [U] 91.59
A:761 [ARG] B:7 [U] 2.69 C:24 [A] 91.59
A:761 [ARG] B:8 [U] 2.74 C:23 [A] 91.59
A:790 [TYR] B:3 [C] 4.39 C:28 [G] 78.02
A:790 [TYR] B:4 [A] 2.6 C:27 [U] 78.02
A:792 [ARG] B:3 [C] 3.38 C:28 [G] 96.46
A:792 [ARG] B:4 [A] 2.77 C:27 [U] 96.46
A:793 [CYS] B:3 [C] 3.22 C:28 [G] 81.74
A:793 [CYS] B:4 [A] 3.71 C:27 [U] 81.74
A:795 [ARG] B:4 [A] 3.31 C:27 [U] sugar:SC 89.74
A:797 [VAL] B:4 [A] 3.9 C:27 [U] 94.87
A:797 [VAL] B:5 [C] 3.85 C:26 [G] 94.87
A:798 [SER] B:4 [A] 4.81 C:27 [U] 98.23
A:798 [SER] B:5 [C] 2.74 C:26 [G] 98.23
A:798 [SER] B:6 [A] 4.53 C:25 [U] 98.23
A:799 [ILE] B:5 [C] 4.87 C:26 [G] 76.61
A:804 [TYR] B:4 [A] 3.49 C:27 [U] 81.49
A:804 [TYR] B:5 [C] 2.69 C:26 [G] 81.49
A:811 [PHE] B:10 [C] 4.33 10.55
A:811 [PHE] C:22 [C] 3.27 B:9 [G] base/AA stacks 10.55
A:812 [ARG] B:1 [U] 3.36 94.19
A:815 [TYR] B:1 [U] 4.02 13.25
A:815 [TYR] C:22 [C] 3.46 B:9 [G] 13.25
A:815 [TYR] C:23 [A] 2.77 B:8 [U] 13.25
A:859 [ALA] B:1 [U] 4.15 69.56
A:859 [ALA] B:3 [C] 4.48 C:28 [G] 69.56

logo_download Export the table of contacts

*Conservation was calculated using Rate4Site
NB: conservation is missing (completly white) for a very small minority of cases in which no homologous sequences were found (e.g. synthetic proteins 7D3J_A & 7EU9_A)

Properties of this interface

Interolog group ID Structure ID Structure description
 UniProt ID
 		ECOD label(s)
 		RFAM label(s)
 		Is ribosome? RCSB PDB link
group140 6CBD_A_B,C A: Protein argonaute-2, Homo sapiens (genetically engineered) B: Guide RNA, Unidentified (synthetic) C: Target RNA, Unidentified (synthetic) Q9UKV8 Ribonuclease H-like & Argonaute, N-terminal domain & SH3 & Middle domain in Argonaute homologs ✘

Interologs

Total number of interologs for this interface: 18

Interface 1 Interface 2 Percentage conservation
 		Interface TM-score
 		Interface RMSD
 		Percentage identity
 		Common ECOD label(s)
 		Common RFAM label(s)
 		Explore both interfaces
4OLA_A_B 6CBD_A_B,C 0.95 0.91 3.17 0.2 Ribonuclease H-like & Argonaute, N-terminal domain & SH3 & Middle domain in Argonaute homologs compare
4KXT_A_B 6CBD_A_B,C 0.91 0.9 2.96 0.17 Ribonuclease H-like & Argonaute, N-terminal domain & SH3 compare
4KRE_A_R 6CBD_A_B,C 0.86 0.93 2.27 0.09 Ribonuclease H-like & Argonaute, N-terminal domain & SH3 & Middle domain in Argonaute homologs compare
5JS1_A_B 6CBD_A_B,C 0.91 0.91 3.24 0.4 Ribonuclease H-like & Argonaute, N-terminal domain & SH3 & Middle domain in Argonaute homologs compare
5AWH_A_C 6CBD_A_B,C 0.59 0.71 3.34 0.16 Ribonuclease H-like & Argonaute, N-terminal domain & SH3 & Middle domain in Argonaute homologs compare
4Z4D_A_B,D 6CBD_A_B,C 0.95 1.0 0.3 0.93 Ribonuclease H-like & Argonaute, N-terminal domain & SH3 & Middle domain in Argonaute homologs compare
4W5O_A_B,D 6CBD_A_B,C 0.99 1.0 0.36 0.97 Ribonuclease H-like & Argonaute, N-terminal domain & SH3 & Middle domain in Argonaute homologs compare
4KRF_A_R 6CBD_A_B,C 0.86 0.93 2.39 0.17 Ribonuclease H-like & Argonaute, N-terminal domain & SH3 & Middle domain in Argonaute homologs compare
4W5T_A_B,D 6CBD_A_B,C 0.94 0.99 0.4 0.88 Ribonuclease H-like & Argonaute, N-terminal domain & SH3 & Middle domain in Argonaute homologs compare
5I4A_A_B 6CBD_A_B,C 0.39 0.78 2.46 0.03 Ribonuclease H-like & Argonaute, N-terminal domain & SH3 & Middle domain in Argonaute homologs compare
4F3T_A_R 6CBD_A_B,C 0.79 0.91 3.2 0.14 Ribonuclease H-like & Argonaute, N-terminal domain & SH3 & Middle domain in Argonaute homologs compare
6CBD_A_B,C 6OZP_A_C,D 0.54 0.61 2.77 0.15 Ribonuclease H-like compare
6CBD_A_B,C 6OZS_B_C,D 0.49 0.63 2.82 0.14 Ribonuclease H-like compare
6CBD_A_B,C 6OZS_A_C,D 0.43 0.61 2.77 0.15 Ribonuclease H-like compare
6CBD_A_B,C 6OON_A_B 0.90 0.95 1.87 0.25 Ribonuclease H-like & Argonaute, N-terminal domain & SH3 & Middle domain in Argonaute homologs compare
6CBD_A_B,C 6D92_A_C 0.57 0.71 3.31 0.11 Ribonuclease H-like & Argonaute, N-terminal domain & SH3 & Middle domain in Argonaute homologs compare
6CBD_A_B,C 6OZP_B_C,D 0.48 0.63 2.7 0.1 Ribonuclease H-like compare
6CBD_A_B,C 6MFN_A_C,E 0.83 0.92 1.43 0.76 Ribonuclease H-like & Argonaute, N-terminal domain & Middle domain in Argonaute homologs compare