MolNFT v1 · #119894 · protein
Crystal structure of a Fab fragment with its ligand peptide
5GIR · Heavy chain of Fab fragment: “Crystal structure of a Fab fragment with its ligand peptide”. X-ray diffraction, 1 ligand (SO4), 9 pockets (best druggability 0.66). MolNFT v1 #119894 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5GIR
- Type
- protein
- Length
- 861 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of Fab fragment; Light chain of Fab fragment…
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.66
Structure
x-ray diffraction · 6 distinct chains · 7% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Heavy chain of Fab fragment | protein | 209 | 9% helix, 50% strand | — |
| L | Light chain of Fab fragment | protein | 212 | 6% helix, 53% strand | — |
| A | Heavy chain of Fab fragment | protein | 207 | 9% helix, 51% strand | — |
| B | Light chain of Fab fragment | protein | 211 | 6% helix, 52% strand | — |
| C | Lys-pro-ile-ile-ile-gly-ser-his-ala-tyr-gly-asp | protein | 12 | 33% helix, 0% strand | — |
| D | Lys-pro-ile-ile-ile-gly-ser-his-ala-tyr-gly-asp | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 9 copies · chains H, L, A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains 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 | 405 | 0.66 | 0.79 | 29 | SO4 |
| 2 | 377 | 0.59 | 0.76 | 38 | empty |
| 3 | 476 | 0.59 | 0.74 | 50 | empty |
| 4 | 95 | 0.39 | 0.77 | 26 | empty |
| 5 | 92 | 0.38 | 0.77 | 24 | empty |
Interfaces
11 interfaces between chains.
- A–B · 1610 Ų buried · 16 hydrogen bonds · protein-protein
- H–L · 1579 Ų buried · 14 hydrogen bonds · protein-protein
- H–C · 426 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 419 Ų buried · 9 hydrogen bonds · protein-protein
- L–C · 333 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 modified (disulfide, cyclization).
Compared structures
- 5GIR · Crystal structure of a Fab fragment with its ligand peptide · 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
- Elsewhere: RCSB PDB 5GIR · PDBe 5GIR
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