MolNFT v1 · #140691 · protein + DNA
Caulobacter crescentus gcra DNA-binding DOMAIN(DBD) in complex with methylated DSDNA(CRYSTAL form 1)
5YIV · Cell cycle regulatory protein gcra: “Caulobacter crescentus gcra DNA-binding DOMAIN(DBD) in complex with methylated DSDNA(CRYSTAL form 1)”. X-ray diffraction. MolNFT v1 #140691 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5YIV
- Type
- protein + DNA
- Length
- 250 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell cycle regulatory protein gcra; DNA (5'-D(*CP*CP*TP*GP*(6MA)P*TP*TP*CP*G)-3'); DNA…
- UniProt
- A0A0H3C9J4
Structure
x-ray diffraction · 4 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cell cycle regulatory protein gcra | protein | 45 | 71% helix, 0% strand | A0A0H3C9J4 |
| E, I | DNA (5'-D(*CP*CP*TP*GP*(6MA)P*TP*TP*CP*G)-3') | dna | 9 | — | — |
| F, H, J, L | DNA (5'-D(*CP*CP*GP*(6MA)P*AP*TP*CP*AP*G)-3') | dna | 9 | — | — |
| G, K | DNA (5'-D(*CP*CP*TP*GP*(6MA)P*TP*TP*CP*G)-3') | dna | 8 | — | — |
Interfaces
25 interfaces between chains.
- C–I · 421 Ų buried · 6 hydrogen bonds · protein-nucleic
- A–E · 410 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–G · 389 Ų buried · 5 hydrogen bonds · protein-nucleic
- K–L · 385 Ų buried · 31 hydrogen bonds · nucleic-nucleic
- G–H · 384 Ų buried · 28 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 8 modified (nucleotide modification).
Compared structures
- 5YIV · Caulobacter crescentus GcrA DNA-binding domain(DBD) in complex with methylated… · the same entry in another collection · chain A against A, 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 A0A0H3C9J4
- Elsewhere: RCSB PDB 5YIV · PDBe 5YIV · UniProt A0A0H3C9J4
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