MolNFT v1 · #152738 · protein + DNA
Complexed crystal structure of passb with ssdna DT25 at 1.91 ångström resolution
6IRQ · Single-stranded DNA-binding protein: “Complexed crystal structure of passb with ssdna DT25 at 1.91 ångström resolution”. X-ray diffraction, 10 pockets (best druggability 0.71). MolNFT v1 #152738 on GenesisL1: 3D structure, binding…
- 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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