MolNFT v1 · #127418 · protein
Fab 4AB007 bound to interleukin-1-beta
5MVZ · Fab 4AB007 H-chain: “Fab 4AB007 bound to interleukin-1-beta”. X-ray diffraction, 9 pockets (best druggability 0.64). MolNFT v1 #127418 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5MVZ
- Type
- protein
- Length
- 1,151 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 4AB007 H-chain; Fab 4AB007 L-chain; Interleukin-1 beta
- UniProt
- B5BUQ8
- Pockets
- 9 · best druggability 0.64
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, A | Fab 4AB007 H-chain | protein | 221 | 8% helix, 53% strand | — |
| L | Fab 4AB007 L-chain | protein | 215 | 7% helix, 54% strand | — |
| U | Interleukin-1 beta | protein | 136 | 2% helix, 52% strand | B5BUQ8 |
| B | Fab 4AB007 L-chain | protein | 214 | 6% helix, 55% strand | — |
| V | Interleukin-1 beta | protein | 144 | 0% helix, 42% strand | B5BUQ8 |
Ligands and binding sites
- GOL · Glycerol · additive · 8 copies · chains H, L, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.64 | 0.74 | 78 | GOL |
| 2 | 291 | 0.59 | 0.78 | 32 | empty |
| 3 | 331 | 0.58 | 0.76 | 38 | empty |
| 4 | 202 | 0.45 | 0.74 | 28 | GOL |
| 5 | 151 | 0.39 | 0.72 | 23 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2133 Ų buried · 17 hydrogen bonds · protein-protein
- H–L · 2084 Ų buried · 20 hydrogen bonds · protein-protein
- H–A · 746 Ų buried · 15 hydrogen bonds · protein-protein
- A–V · 593 Ų buried · 9 hydrogen bonds · protein-protein
- H–U · 575 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide (disulfide).
Compared structures
- 5MVZ · Fab 4AB007 bound to Interleukin-1-beta · the same entry in another collection · chain H against H, 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 B5BUQ8
- Elsewhere: RCSB PDB 5MVZ · PDBe 5MVZ · UniProt B5BUQ8
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