MolNFT v1 · #85649 · protein
Crystallographic structure of 3MJL2 from the germinal line lambda 3
4AIZ · V2-17 protein: “Crystallographic structure of 3MJL2 from the germinal line lambda 3”. X-ray diffraction, 2 ligands (88Q, SO4), 7 pockets (best druggability 0.69). MolNFT v1 #85649 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4AIZ
- Type
- protein
- Length
- 426 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- V2-17 protein
- UniProt
- Q5NV90
- Ligands
- 88Q, SO4
- Pockets
- 7 · best druggability 0.69
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | V2-17 protein | protein | 107 | 6% helix, 47% strand | Q5NV90 |
| B | V2-17 protein | protein | 106 | 3% helix, 49% strand | Q5NV90 |
| D | V2-17 protein | protein | 106 | 3% helix, 47% strand | Q5NV90 |
Ligands and binding sites
- 88Q · 1,5:6,10-dianhydro-3,4,7,8-tetradeoxy-2,9-bis-C-(hydroxymethyl)-L-manno-decitol · ligand · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, B, C
- CIT · Citric acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 75 | 0.69 | 0.95 | 26 | 88Q |
| 2 | 324 | 0.61 | 0.78 | 50 | empty |
| 3 | 170 | 0.60 | 0.83 | 34 | empty |
| 4 | 112 | 0.42 | 0.76 | 21 | empty |
| 5 | 94 | 0.38 | 0.76 | 15 | CIT |
Interfaces
6 interfaces between chains.
- A–B · 980 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 960 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 404 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 310 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 170 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4AIZ · Crystallographic structure of 3mJL2 from the germinal line lambda 3 · 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 Q5NV90
- Elsewhere: RCSB PDB 4AIZ · PDBe 4AIZ · UniProt Q5NV90
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