MolNFT v1 · #69206 · protein
Crystal structure of NMB1025, a member of yjgf protein family, from neisseria meningitidis (monoclinic crystal form)
3KJK · NMB1025 protein: “Crystal structure of NMB1025, a member of yjgf protein family, from neisseria meningitidis (monoclinic…”. X-ray diffraction, 20 pockets (best druggability 0.84). MolNFT v1 #69206 on GenesisL1: 3D structure, binding…
- PDB
- 3KJK
- Type
- protein
- Length
- 1,394 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NMB1025 protein
- UniProt
- Q9JZJ4
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, E, F, G, H, I, J, K | NMB1025 protein | protein | 116 | 30% helix, 34% strand | Q9JZJ4 |
| D, L | NMB1025 protein | protein | 117 | 30% helix, 34% strand | Q9JZJ4 |
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 279 | 0.84 | 0.96 | 30 | empty |
| 2 | 240 | 0.82 | 0.95 | 30 | empty |
| 3 | 86 | 0.76 | 0.98 | 23 | empty |
| 4 | 74 | 0.76 | 0.98 | 21 | empty |
| 5 | 72 | 0.74 | 0.98 | 23 | empty |
Interfaces
27 interfaces between chains.
- D–E · 1150 Ų buried · 20 hydrogen bonds · protein-protein
- J–K · 1146 Ų buried · 22 hydrogen bonds · protein-protein
- K–L · 1146 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1141 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 1139 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 modified (engineered).
Compared structures
- 3KJK · Crystal structure of NMB1025, a member of YjgF protein family, from Neisseria… · the same entry in another collection · chain F against F, 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 Q9JZJ4
- Elsewhere: RCSB PDB 3KJK · PDBe 3KJK · UniProt Q9JZJ4
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