Research workbench
Structure of a yeast closed complex with distorted DNA (core ccdist)
Analyse Structure of a yeast closed complex with distorted DNA (core ccdist) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GYL
- Type
- protein + DNA
- Length
- 5,362 residues
- Chains
- 22
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase II subunit RPB1; DNA-directed RNA polymerase II subunit RPB2…
- EC
- 2.7.7.6, 3.6.4.12
- UniProt
- P04050, P08518, P16370, P20433, P20434, P20435, P34087, P20436, P27999, P22139, P38902, P40422, P29055, P13393, P41895, P41896, P32773, P32774, P36100, P36145
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 22 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase II subunit RPB1 (EC 2.7.7.6) | protein | 1398 | 41% helix, 16% strand | P04050 |
| B | DNA-directed RNA polymerase II subunit RPB2 (EC 2.7.7.6) | protein | 1152 | 29% helix, 25% strand | P08518 |
| C | DNA-directed RNA polymerase II subunit RPB3 | protein | 262 | 25% helix, 27% strand | P16370 |
| D | DNA-directed RNA polymerase II subunit RPB4 | protein | 157 | 54% helix, 5% strand | P20433 |
| E | DNA-directed RNA polymerases I, II, and III subunit RPABC1 | protein | 213 | 41% helix, 22% strand | P20434 |
| F | DNA-directed RNA polymerases I, II, and III subunit RPABC2 | protein | 83 | 35% helix, 16% strand | P20435 |
| G | DNA-directed RNA polymerase II subunit RPB7 | protein | 171 | 13% helix, 50% strand | P34087 |
| H | DNA-directed RNA polymerases I, II, and III subunit RPABC3 | protein | 136 | 0% helix, 49% strand | P20436 |
| I | DNA-directed RNA polymerase II subunit RPB9 | protein | 116 | 4% helix, 27% strand | P27999 |
| J | DNA-directed RNA polymerases I, II, and III subunit RPABC5 | protein | 65 | 54% helix, 2% strand | P22139 |
| K | DNA-directed RNA polymerase II subunit RPB11 | protein | 112 | 39% helix, 25% strand | P38902 |
| L | DNA-directed RNA polymerases I, II, and III subunit RPABC4 | protein | 45 | 0% helix, 20% strand | P40422 |
| M | Transcription initiation factor iib | protein | 279 | 57% helix, 5% strand | P29055 |
| N | GAT1 promoter DNA | dna | 56 | — | — |
| O | Tata-box-binding protein | protein | 180 | 27% helix, 37% strand | P13393 |
| Q | Transcription initiation factor iif subunit alpha | protein | 148 | 18% helix, 33% strand | P41895 |
| R | Transcription initiation factor iif subunit beta (EC 3.6.4.12) | protein | 190 | 30% helix, 31% strand | P41896 |
| T | GAT1 promoter DNA | dna | 56 | — | — |
| U | Transcription initiation factor iia large subunit, transcription initiation factor iia large subunit | protein | 92 | 43% helix, 42% strand | P32773 |
| V | Transcription initiation factor iia subunit 2 | protein | 100 | 38% helix, 39% strand | P32774 |
| W | Transcription initiation factor iie subunit ALPHA,TFA1, TFA1 | protein | 191 | 57% helix, 10% strand | P36100 |
| X | Transcription initiation factor iie subunit beta | protein | 160 | 43% helix, 5% strand | P36145 |
Ligands and binding sites
- ZN · Zinc ion · metal · 10 copies · chains A, B, C, I, J, L, M, W
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.88 | 0.89 | 113 | empty |
| 2 | 959 | 0.84 | 0.86 | 104 | empty |
| 3 | 919 | 0.84 | 0.86 | 98 | empty |
| 4 | 1163 | 0.84 | 0.85 | 94 | empty |
| 5 | 1119 | 0.82 | 0.83 | 104 | empty |
Interfaces
59 interfaces between chains.
- A–B · 9918 Ų buried · 121 hydrogen bonds · protein-protein
- A–M · 2729 Ų buried · 30 hydrogen bonds · protein-protein
- U–V · 2597 Ų buried · 22 hydrogen bonds · protein-protein
- N–T · 2516 Ų buried · 171 hydrogen bonds · nucleic-nucleic
- Q–R · 2132 Ų buried · 38 hydrogen bonds · protein-protein
Compared structures
- 6GYL · Structure of a yeast closed complex with distorted DNA (core CCdist) · the same entry in another collection · chain G against G, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P04050
- Every structure of UniProt P08518
- Every structure of UniProt P16370
- Every structure of UniProt P20433
- Every structure of UniProt P20434
- Every structure of UniProt P20435
- Every structure of UniProt P34087
- Every structure of UniProt P20436
- Every structure of UniProt P27999
- Every structure of UniProt P22139
- Every structure of UniProt P38902
- Every structure of UniProt P40422
- Every structure of UniProt P29055
- Every structure of UniProt P13393
- Every structure of UniProt P41895
- Every structure of UniProt P41896
- Every structure of UniProt P32773
- Every structure of UniProt P32774
- Every structure of UniProt P36100
- Every structure of UniProt P36145
- Elsewhere: RCSB PDB 6GYL · PDBe 6GYL · UniProt P04050 · UniProt P08518 · UniProt P16370 · UniProt P20433 · UniProt P20434 · UniProt P20435 · UniProt P34087 · UniProt P20436 · UniProt P27999 · UniProt P22139 · UniProt P38902 · UniProt P40422 · UniProt P29055 · UniProt P13393 · UniProt P41895 · UniProt P41896 · UniProt P32773 · UniProt P32774 · UniProt P36100 · UniProt P36145
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