MolNFT v1 · #162050 · protein + DNA
3.4A structure of benzoisoxazole 3 with S.AUREUS DNA gyrase and DNA
6QX2 · DNA gyrase subunit B,DNA gyrase subunit B: “3.4A structure of benzoisoxazole 3 with S.AUREUS DNA gyrase and DNA”. X-ray diffraction, 1 ligand (JK8), 20 pockets (best druggability 0.83). MolNFT v1 #162050 on GenesisL1: 3D structure…
- PDB
- 6QX2
- Type
- protein + DNA
- Length
- 8,238 residues
- Chains
- 36
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA gyrase subunit B,DNA gyrase subunit B; DNA gyrase subunit a; DNA (5'…
- EC
- 5.99.1.3
- UniProt
- P0A0K8, P66936, Q99XG5, Q6GKU0, P66937, Q2FKQ1
- Ligands
- JK8
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 20 distinct chains · 48% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, b | DNA gyrase subunit B,DNA gyrase subunit B (EC 5.99.1.3) | protein | 185 | 48% helix, 11% strand | P0A0K8, P66936 |
| A | DNA gyrase subunit a (EC 5.99.1.3) | protein | 479 | 49% helix, 17% strand | Q99XG5 |
| D, U, m | DNA gyrase subunit B,DNA gyrase subunit B (EC 5.99.1.3) | protein | 188 | 47% helix, 11% strand | P0A0K8, Q6GKU0 |
| C, c | DNA gyrase subunit a (EC 5.99.1.3) | protein | 482 | 49% helix, 17% strand | Q99XG5 |
| E, F, N, O, V, e, n | DNA (5'- D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') | dna | 19 | — | — |
| K | DNA gyrase subunit B,DNA gyrase subunit B (EC 5.99.1.3) | protein | 187 | 48% helix, 11% strand | P66937, Q2FKQ1 |
| J | DNA gyrase subunit a (EC 5.99.1.3) | protein | 480 | 49% helix, 17% strand | Q99XG5 |
| M | DNA gyrase subunit B,DNA gyrase subunit B (EC 5.99.1.3) | protein | 189 | 47% helix, 11% strand | P66937, Q2FKQ1 |
| L, T, l, t | DNA gyrase subunit a (EC 5.99.1.3) | protein | 481 | 48% helix, 18% strand | Q99XG5 |
| S | DNA gyrase subunit B,DNA gyrase subunit B (EC 5.99.1.3) | protein | 184 | 48% helix, 11% strand | P0A0K8, P66936 |
| R, j | DNA gyrase subunit a (EC 5.99.1.3) | protein | 482 | 49% helix, 18% strand | Q99XG5 |
| W, w | DNA (5'- D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') | dna | 20 | — | — |
| a | DNA gyrase subunit a (EC 5.99.1.3) | protein | 481 | 49% helix, 18% strand | Q99XG5 |
| d | DNA gyrase subunit B,DNA gyrase subunit B (EC 5.99.1.3) | protein | 181 | 49% helix, 12% strand | Q6GKU0, P66937 |
| f | DNA (5'- D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') | dna | 17 | — | — |
| k | DNA gyrase subunit B,DNA gyrase subunit B (EC 5.99.1.3) | protein | 188 | 47% helix, 11% strand | Q6GKU0, P66937 |
| o, v | DNA (5'- D(*GP*AP*GP*CP*GP*TP*AP*CP*GP*GP*CP*CP*GP*TP*AP*CP*GP*CP*TP*T)-3') | dna | 18 | — | — |
| s | DNA gyrase subunit B,DNA gyrase subunit B (EC 5.99.1.3) | protein | 186 | 48% helix, 11% strand | P0A0K8, P66936 |
| r | DNA gyrase subunit a (EC 5.99.1.3) | protein | 484 | 49% helix, 18% strand | Q99XG5 |
| u | DNA gyrase subunit B,DNA gyrase subunit B (EC 5.99.1.3) | protein | 187 | 47% helix, 11% strand | P66937, Q2FKQ1 |
Ligands and binding sites
- JK8 · (2~{R})-2-[[5-(2-chlorophenyl)-1,2-benzoxazol-3-yl]oxy]-2-phenyl-ethanamine · ligand · 12 copies · chains B, A, D, C, K, J, l, M, L, S, R, U, T, b, a, d, c, k, j, m, s, r, u, t
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1106 | 0.83 | 0.85 | 124 | empty |
| 2 | 923 | 0.83 | 0.85 | 110 | empty |
| 3 | 940 | 0.83 | 0.84 | 100 | empty |
| 4 | 974 | 0.82 | 0.84 | 97 | empty |
| 5 | 928 | 0.82 | 0.84 | 105 | empty |
Interfaces
98 interfaces between chains.
- r–t · 1736 Ų buried · 29 hydrogen bonds · protein-protein
- R–T · 1735 Ų buried · 20 hydrogen bonds · protein-protein
- j–l · 1720 Ų buried · 24 hydrogen bonds · protein-protein
- a–c · 1682 Ų buried · 21 hydrogen bonds · protein-protein
- J–L · 1671 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 6QX2 · 3.4A structure of benzoisoxazole 3 with S.aureus DNA gyrase and DNA · the same entry in another collection · chain N against N, 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 P0A0K8
- Every structure of UniProt P66936
- Every structure of UniProt Q99XG5
- Every structure of UniProt Q6GKU0
- Every structure of UniProt P66937
- Every structure of UniProt Q2FKQ1
- Elsewhere: RCSB PDB 6QX2 · PDBe 6QX2 · UniProt P0A0K8 · UniProt P66936 · UniProt Q99XG5 · UniProt Q6GKU0 · UniProt P66937 · UniProt Q2FKQ1
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