MolNFT v1 · #137861 · protein
Junv GP1 CR1-10 Fab CR1-28 Fab complex
5W1K · CR1-28 Fab light chain: “Junv GP1 CR1-10 Fab CR1-28 Fab complex”. X-ray diffraction, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.70). MolNFT v1 #137861 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5W1K
- Type
- protein
- Length
- 4,045 residues
- Chains
- 20
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CR1-28 Fab light chain; CR1-28 Fab heavy chain; CR1-10 Fab light chain; CR1-10 Fab heavy…
- UniProt
- P0DOX7, S6C4R2, Q6PIL8, S6B2B6, P26313
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 7 distinct chains · 9% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, K, S | CR1-28 Fab light chain | protein | 206 | 7% helix, 44% strand | P0DOX7 |
| B, G, L, T | CR1-28 Fab heavy chain | protein | 226 | 3% helix, 43% strand | S6C4R2 |
| C, H, M | CR1-10 Fab light chain | protein | 213 | 8% helix, 50% strand | Q6PIL8 |
| D, I, O, Q | CR1-10 Fab heavy chain | protein | 225 | 3% helix, 44% strand | S6B2B6 |
| E, P, R | Pre-glycoprotein polyprotein gp complex | protein | 142 | 23% helix, 25% strand | P26313 |
| J | Pre-glycoprotein polyprotein gp complex | protein | 141 | 23% helix, 25% strand | P26313 |
| N | CR1-10 Fab light chain | protein | 211 | 6% helix, 50% strand | Q6PIL8 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains E, F, J, K, A, P, R, S, O
- BMA · beta-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1054 | 0.70 | 0.74 | 105 | empty |
| 2 | 919 | 0.68 | 0.74 | 83 | empty |
| 3 | 618 | 0.64 | 0.75 | 80 | empty |
| 4 | 318 | 0.63 | 0.80 | 40 | empty |
| 5 | 597 | 0.63 | 0.74 | 71 | empty |
Interfaces
32 interfaces between chains.
- N–O · 2132 Ų buried · 22 hydrogen bonds · protein-protein
- H–I · 2076 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 2039 Ų buried · 21 hydrogen bonds · protein-protein
- M–Q · 2032 Ų buried · 22 hydrogen bonds · protein-protein
- K–L · 1943 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 5W1K · JUNV GP1 CR1-10 Fab CR1-28 Fab complex · the same entry in another collection · chain T against T, 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 P0DOX7
- Every structure of UniProt S6C4R2
- Every structure of UniProt Q6PIL8
- Every structure of UniProt S6B2B6
- Every structure of UniProt P26313
- Elsewhere: RCSB PDB 5W1K · PDBe 5W1K · UniProt P0DOX7 · UniProt S6C4R2 · UniProt Q6PIL8 · UniProt S6B2B6 · UniProt P26313
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