MolNFT v1 · #115242 · protein + DNA
2.65 structure of S.AUREUS DNA gyrase and artificially nicked DNA
5CDR · DNA gyrase subunit a: “2.65 structure of S.AUREUS DNA gyrase and artificially nicked DNA”. X-ray diffraction, 1 ligand (MN), 16 pockets (best druggability 0.78). MolNFT v1 #115242 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5CDR
- Type
- protein + DNA
- Length
- 1,379 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit a; DNA gyrase subunit B,DNA gyrase subunit B; DNA…
- EC
- 5.99.1.3
- UniProt
- Q99XG5, P66937
- Ligands
- MN
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 7 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA gyrase subunit a (EC 5.99.1.3) | protein | 483 | 48% helix, 18% strand | Q99XG5 |
| B | DNA gyrase subunit B,DNA gyrase subunit B (EC 5.99.1.3) | protein | 190 | 47% helix, 13% strand | P66937 |
| C | DNA gyrase subunit a (EC 5.99.1.3) | protein | 481 | 48% helix, 18% strand | Q99XG5 |
| D | DNA gyrase subunit B,DNA gyrase subunit B (EC 5.99.1.3) | protein | 189 | 47% helix, 13% strand | P66937 |
| E | DNA (5'-D(*AP*GP*CP*CP*GP*TP*AP*)-3') | dna | 8 | — | — |
| G | DNA (5'-D(*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3') | dna | 12 | — | — |
| F | DNA (5'- D(*AP*GP*CP*CP*GP*TP*AP*GP*GP*TP*AP*CP*CP*TP*AP*CP*GP*GP*CP*T)-3') | dna | 16 | — | — |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 3 copies · chains A, B, D
- GOL · Glycerol · additive · 6 copies · chains A, C, E, G, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1093 | 0.78 | 0.80 | 107 | MN, GOL |
| 2 | 446 | 0.73 | 0.83 | 33 | empty |
| 3 | 278 | 0.73 | 0.87 | 44 | GOL |
| 4 | 454 | 0.72 | 0.82 | 33 | empty |
| 5 | 440 | 0.69 | 0.80 | 67 | MN |
Interfaces
18 interfaces between chains.
- A–C · 1714 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1538 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1530 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 662 Ų buried · 8 hydrogen bonds · protein-protein
- A–E · 647 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 5CDR · 2.65 structure of S.aureus DNA gyrase and artificially nicked DNA · the same entry in another collection · chain F against F, TM-score 1.00
- P66937 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit B (P66937) · a predicted model of the same protein · chain D against A, TM-score 0.98
- Q99XG5 · AlphaFold monomer V2.0 prediction for DNA gyrase subunit a (Q99XG5) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q99XG5
- Every structure of UniProt P66937
- Elsewhere: RCSB PDB 5CDR · PDBe 5CDR · UniProt Q99XG5 · UniProt P66937
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