Research workbench
Crystal structure of megabody mb-NB207-C7HOPQ_G10
Analyse Crystal structure of megabody mb-NB207-C7HOPQ_G10 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XV8
- Type
- protein
- Length
- 1,640 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein
- UniProt
- B5Z8H1
- Pockets
- 15 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Outer membrane protein | protein | 412 | 42% helix, 20% strand | B5Z8H1 |
| B | Outer membrane protein | protein | 429 | 44% helix, 22% strand | B5Z8H1 |
| C | Outer membrane protein | protein | 412 | 42% helix, 21% strand | B5Z8H1 |
| D | Outer membrane protein | protein | 387 | 43% helix, 21% strand | B5Z8H1 |
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 985 | 0.82 | 0.83 | 108 | empty |
| 2 | 354 | 0.67 | 0.81 | 40 | empty |
| 3 | 437 | 0.66 | 0.79 | 61 | empty |
| 4 | 183 | 0.59 | 0.82 | 25 | empty |
| 5 | 125 | 0.58 | 0.84 | 22 | empty |
Interfaces
5 interfaces between chains.
- B–C · 988 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 290 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 175 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 63 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 10 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 6XV8 · Crystal structure of Megabody Mb-Nb207-c7HopQ_G10 · 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 B5Z8H1
- Elsewhere: RCSB PDB 6XV8 · PDBe 6XV8 · UniProt B5Z8H1
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