MolNFT v1 · #115505 · protein + DNA
Crystal structure of kora-operator DNA complex (kora-oa)
5CLV · Trfb transcriptional repressor protein: “Crystal structure of kora-operator DNA complex (kora-oa)”. X-ray diffraction, 13 pockets (best druggability 0.61). MolNFT v1 #115505 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5CLV
- Type
- protein + DNA
- Length
- 724 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Trfb transcriptional repressor protein; 5'-D(CP*CP*AP*AP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*…
- UniProt
- P03052
- Pockets
- 13 · best druggability 0.61
Structure
x-ray diffraction · 8 distinct chains · 65% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trfb transcriptional repressor protein | protein | 95 | 61% helix, 8% strand | P03052 |
| B | Trfb transcriptional repressor protein | protein | 96 | 63% helix, 8% strand | P03052 |
| C, D, G, H, K, L, O, P | 5'-D(CP*CP*AP*AP*GP*TP*TP*TP*AP*GP*CP*TP*AP*AP*AP*CP*TP*TP* GP*GP*)-3' | dna | 19 | — | — |
| E | Trfb transcriptional repressor protein | protein | 65 | 68% helix, 0% strand | P03052 |
| F, N | Trfb transcriptional repressor protein | protein | 64 | 67% helix, 0% strand | P03052 |
| I | Trfb transcriptional repressor protein | protein | 62 | 68% helix, 0% strand | P03052 |
| J | Trfb transcriptional repressor protein | protein | 63 | 67% helix, 0% strand | P03052 |
| M | Trfb transcriptional repressor protein | protein | 63 | 68% helix, 0% strand | P03052 |
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 471 | 0.61 | 0.76 | 42 | empty |
| 2 | 433 | 0.59 | 0.75 | 43 | empty |
| 3 | 373 | 0.56 | 0.75 | 39 | empty |
| 4 | 320 | 0.54 | 0.75 | 29 | empty |
| 5 | 337 | 0.52 | 0.73 | 29 | empty |
Interfaces
26 interfaces between chains.
- A–B · 1128 Ų buried · 16 hydrogen bonds · protein-protein
- O–P · 821 Ų buried · 80 hydrogen bonds · nucleic-nucleic
- K–L · 819 Ų buried · 77 hydrogen bonds · nucleic-nucleic
- G–H · 803 Ų buried · 73 hydrogen bonds · nucleic-nucleic
- C–D · 793 Ų buried · 75 hydrogen bonds · nucleic-nucleic
Compared structures
- P03052 · AlphaFold monomer V2.0 prediction for trfb transcriptional repressor protein (P03052) · a predicted model of the same protein · chain F against A, TM-score 0.99
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 P03052
- Elsewhere: RCSB PDB 5CLV · PDBe 5CLV · UniProt P03052
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