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Interphotoreceptor retinoid-binding protein (irbp) in complex with a monoclonal antibody (F3F5 MAB5)
Analyse Interphotoreceptor retinoid-binding protein (irbp) in complex with a monoclonal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JTI
- Type
- protein
- Length
- 1,639 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MAB5 Fab light chain; MAB5 Fab heavy chain; Retinol-binding protein 3
- UniProt
- P12661
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 6 distinct chains · 28% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | MAB5 Fab light chain | protein | 210 | 8% helix, 55% strand | — |
| H | MAB5 Fab heavy chain | protein | 221 | 3% helix, 51% strand | — |
| A | Retinol-binding protein 3 | protein | 303 | 36% helix, 20% strand | P12661 |
| B | Retinol-binding protein 3 | protein | 309 | 39% helix, 21% strand | — |
| C | Retinol-binding protein 3 | protein | 300 | 37% helix, 21% strand | P12661 |
| D | Retinol-binding protein 3 | protein | 296 | 35% helix, 22% strand | P12661 |
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 296 | 0.83 | 0.93 | 28 | empty |
| 2 | 308 | 0.78 | 0.88 | 38 | empty |
| 3 | 427 | 0.72 | 0.82 | 62 | empty |
| 4 | 195 | 0.71 | 0.88 | 21 | empty |
| 5 | 117 | 0.68 | 0.90 | 31 | empty |
Interfaces
6 interfaces between chains.
- L–H · 1778 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 630 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 584 Ų buried · 36 hydrogen bonds · protein-protein
- C–D · 538 Ų buried · 48 hydrogen bonds · protein-protein
- H–A · 451 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7JTI · Interphotoreceptor retinoid-binding protein (IRBP) in complex with a monoclonal antibody… · the same entry in another collection · chain D against D, TM-score 1.00
- P12661 · AlphaFold monomer V2.0 prediction for retinol-binding protein 3 (P12661) · a predicted model of the same protein · chain D against A, TM-score 0.91
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 P12661
- Elsewhere: RCSB PDB 7JTI · PDBe 7JTI · UniProt P12661
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