Research workbench
Complexed crystal structure of passb with ssdna DT25 at 1.91 ångström resolution
Analyse Complexed crystal structure of passb with ssdna DT25 at 1.91 ångström resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6IRQ
- Type
- protein + DNA
- Length
- 437 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Single-stranded DNA-binding protein; DNA (25-mer)
- UniProt
- P40947
- Pockets
- 10 · best druggability 0.71
Structure
x-ray diffraction · 6 distinct chains · 9% helix, 61% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Single-stranded DNA-binding protein | protein | 103 | 9% helix, 62% strand | P40947 |
| B | Single-stranded DNA-binding protein | protein | 101 | 9% helix, 61% strand | P40947 |
| C | Single-stranded DNA-binding protein | protein | 104 | 10% helix, 60% strand | P40947 |
| D | Single-stranded DNA-binding protein | protein | 103 | 9% helix, 61% strand | P40947 |
| E | DNA (25-mer) | dna | 14 | — | — |
| F | DNA (25-mer) | dna | 12 | — | — |
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 650 | 0.71 | 0.79 | 47 | empty |
| 2 | 330 | 0.64 | 0.80 | 35 | empty |
| 3 | 315 | 0.63 | 0.80 | 40 | empty |
| 4 | 316 | 0.62 | 0.79 | 38 | empty |
| 5 | 277 | 0.61 | 0.80 | 29 | empty |
Interfaces
14 interfaces between chains.
- C–D · 1199 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1092 Ų buried · 17 hydrogen bonds · protein-protein
- A–F · 593 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–E · 526 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–F · 486 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- 6IRQ · Complexed crystal structure of PaSSB with ssDNA dT25 at 1.91 angstrom resolution · the same entry in another collection · chain F against F, TM-score 1.00
- P40947 · AlphaFold monomer V2.0 prediction for single-stranded DNA-binding protein (P40947) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P40947
- Elsewhere: RCSB PDB 6IRQ · PDBe 6IRQ · UniProt P40947
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