MolNFT v1 · #146715 · protein
Crystal structure of neisseria meningitidis dsbd N-terminal domain in the oxidised form
6DPS · THIOL:DISULFIDE interchange protein dsbd: “Crystal structure of neisseria meningitidis dsbd N-terminal domain in the oxidised form”. X-ray diffraction, 1 ligand (ZN), 11 pockets (best druggability 0.80). MolNFT v1 #146715 on…
- PDB
- 6DPS
- Type
- protein
- Length
- 732 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- THIOL:DISULFIDE interchange protein dsbd
- EC
- 1.8.1.8
- UniProt
- C6S7X6
- Ligands
- ZN
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | THIOL:DISULFIDE interchange protein dsbd (EC 1.8.1.8) | protein | 122 | 6% helix, 56% strand | C6S7X6 |
| C | THIOL:DISULFIDE interchange protein dsbd (EC 1.8.1.8) | protein | 123 | 6% helix, 54% strand | C6S7X6 |
| D | THIOL:DISULFIDE interchange protein dsbd (EC 1.8.1.8) | protein | 124 | 6% helix, 53% strand | C6S7X6 |
| E | THIOL:DISULFIDE interchange protein dsbd (EC 1.8.1.8) | protein | 121 | 6% helix, 52% strand | C6S7X6 |
| F | THIOL:DISULFIDE interchange protein dsbd (EC 1.8.1.8) | protein | 120 | 3% helix, 56% strand | C6S7X6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 32 copies · chains A, C, D, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1025 | 0.80 | 0.82 | 130 | ZN |
| 2 | 806 | 0.77 | 0.81 | 89 | ZN |
| 3 | 318 | 0.62 | 0.79 | 37 | empty |
| 4 | 187 | 0.57 | 0.80 | 26 | empty |
| 5 | 117 | 0.47 | 0.79 | 27 | empty |
Interfaces
9 interfaces between chains.
- C–F · 554 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 521 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 517 Ų buried · 13 hydrogen bonds · protein-protein
- A–F · 513 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 473 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 6DPS · Crystal Structure of Neisseria meningitidis DsbD n-terminal domain in the oxidised form · 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 C6S7X6
- Elsewhere: RCSB PDB 6DPS · PDBe 6DPS · UniProt C6S7X6
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