Research workbench
Crystal structure of PA4674 in complex with its operator DNA (18BP) from pseudomonas aeruginosa
Analyse Crystal structure of PA4674 in complex with its operator DNA (18BP) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LB3
- Type
- protein + DNA
- Length
- 821 residues
- Chains
- 14
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hth CRO/C1-type domain-containing protein; DNA (5'…
- UniProt
- Q9HVC1
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 11 distinct chains · 64% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hth CRO/C1-type domain-containing protein | protein | 91 | 70% helix, 0% strand | Q9HVC1 |
| B, C | Hth CRO/C1-type domain-containing protein | protein | 93 | 66% helix, 0% strand | Q9HVC1 |
| D | Hth CRO/C1-type domain-containing protein | protein | 92 | 64% helix, 0% strand | Q9HVC1 |
| E | Hth CRO/C1-type domain-containing protein | protein | 90 | 59% helix, 0% strand | Q9HVC1 |
| F | Hth CRO/C1-type domain-containing protein | protein | 93 | 65% helix, 0% strand | Q9HVC1 |
| G | Hth CRO/C1-type domain-containing protein | protein | 88 | 59% helix, 0% strand | Q9HVC1 |
| H | Hth CRO/C1-type domain-containing protein | protein | 95 | 62% helix, 0% strand | Q9HVC1 |
| I, K | DNA (5'- D(P*AP*CP*GP*CP*TP*TP*AP*AP*CP*GP*TP*TP*AP*AP*GP*GP*GP*T)-3') | dna | 18 | — | — |
| J, L | DNA (5'- D(P*AP*CP*CP*CP*TP*TP*AP*AP*CP*GP*TP*TP*AP*AP*GP*CP*GP*T)-3') | dna | 18 | — | — |
| M | DNA (5'- D(P*AP*CP*GP*CP*TP*TP*AP*AP*CP*GP*TP*TP*AP*AP*GP*GP*GP*T)-3') | dna | 7 | — | — |
| N | DNA (5'- D(P*AP*CP*CP*CP*TP*TP*AP*AP*CP*GP*TP*TP*AP*AP*GP*CP*GP*T)-3') | dna | 7 | — | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 801 | 0.77 | 0.81 | 56 | empty |
| 2 | 751 | 0.76 | 0.81 | 56 | empty |
| 3 | 556 | 0.67 | 0.78 | 37 | empty |
| 4 | 512 | 0.66 | 0.78 | 32 | empty |
| 5 | 134 | 0.47 | 0.78 | 23 | empty |
Interfaces
27 interfaces between chains.
- A–B · 1484 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1474 Ų buried · 13 hydrogen bonds · protein-protein
- G–H · 1441 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 1417 Ų buried · 12 hydrogen bonds · protein-protein
- K–L · 794 Ų buried · 74 hydrogen bonds · nucleic-nucleic
Compared structures
- 6LB3 · Crystal structure of PA4674 in complex with its operator DNA (18bp) from Pseudomonas… · the same entry in another collection · chain I against I, 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 Q9HVC1
- Elsewhere: RCSB PDB 6LB3 · PDBe 6LB3 · UniProt Q9HVC1
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