Research workbench
Crystal structure of T. thermophilus TTHB099 class II transcription activation complex: tap-rpo
Analyse Crystal structure of T. thermophilus TTHB099 class II transcription activation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I2D
- Type
- protein + DNA + RNA
- Length
- 8,008 residues
- Chains
- 22
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase subunit beta…
- EC
- 2.7.7.6
- UniProt
- Q5SHR6, Q8RQE9, Q8RQE8, Q8RQE7, Q5SKW1, Q53W63
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 10 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, L | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 284 | 30% helix, 33% strand | Q5SHR6 |
| B, M | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 280 | 31% helix, 35% strand | Q5SHR6 |
| C, N | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1111 | 29% helix, 26% strand | Q8RQE9 |
| D, O | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1363 | 40% helix, 21% strand | Q8RQE8 |
| E, P | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 94 | 49% helix, 11% strand | Q8RQE7 |
| F, Q | RNA polymerase sigma factor siga | protein | 346 | 69% helix, 1% strand | Q5SKW1 |
| G, H, R, S | Transcriptional regulator, crp family | protein | 195 | 37% helix, 29% strand | Q53W63 |
| I, T | DNA (72-mer) | dna | 66 | — | — |
| J, U | DNA (72-mer) | dna | 66 | — | — |
| K, V | RNA (5'-R(*UP*CP*GP*A)-3') | rna | 4 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains D, O
- MG · Magnesium ion · metal · 2 copies · chains D, K, O, V
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 | 875 | 0.87 | 0.89 | 104 | empty |
| 2 | 1143 | 0.86 | 0.87 | 137 | empty |
| 3 | 919 | 0.85 | 0.87 | 87 | empty |
| 4 | 620 | 0.85 | 0.90 | 70 | empty |
| 5 | 660 | 0.85 | 0.90 | 83 | empty |
Interfaces
64 interfaces between chains.
- C–D · 9117 Ų buried · 122 hydrogen bonds · protein-protein
- N–O · 9080 Ų buried · 124 hydrogen bonds · protein-protein
- D–F · 4113 Ų buried · 59 hydrogen bonds · protein-protein
- O–Q · 4063 Ų buried · 58 hydrogen bonds · protein-protein
- C–F · 2506 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5I2D · Crystal structure of T. thermophilus TTHB099 class II transcription activation complex… · the same entry in another collection · chain V against V, 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 Q5SHR6
- Every structure of UniProt Q8RQE9
- Every structure of UniProt Q8RQE8
- Every structure of UniProt Q8RQE7
- Every structure of UniProt Q5SKW1
- Every structure of UniProt Q53W63
- Elsewhere: RCSB PDB 5I2D · PDBe 5I2D · UniProt Q5SHR6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q8RQE7 · UniProt Q5SKW1 · UniProt Q53W63
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