MolNFT v1 · #61965 · protein
Crystal structure of BBETAD432A variant fibrinogen fragment D with the peptide ligand gly-his-arg-pro-amide
3E1I · Fibrinogen alpha chain: “Crystal structure of BBETAD432A variant fibrinogen fragment D with the peptide ligand gly-his-arg-pro-amide”. X-ray diffraction, 2 ligands (NAG, CA), 19 pockets (best druggability 0.65). MolNFT v1 #61965 on…
- PDB
- 3E1I
- Type
- protein
- Length
- 1,291 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibrinogen alpha chain; Fibrinogen beta chain; Fibrinogen gamma chain…
- UniProt
- P02671, P02675, P02679
- Ligands
- NAG, CA
- Pockets
- 19 · best druggability 0.65
Structure
x-ray diffraction · 6 distinct chains · 24% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fibrinogen alpha chain | protein | 57 | 51% helix, 2% strand | P02671 |
| B, E | Fibrinogen beta chain | protein | 298 | 20% helix, 27% strand | P02675 |
| C | Fibrinogen gamma chain | protein | 288 | 22% helix, 25% strand | P02679 |
| D | Fibrinogen alpha chain | protein | 54 | 48% helix, 2% strand | P02671 |
| F | Fibrinogen gamma chain | protein | 288 | 22% helix, 25% strand | P02679 |
| G, H | Gly-his-arg-pro-amide | protein | 4 | 0% helix, 25% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains B, E
- CA · Calcium ion · metal · 7 copies · chains B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 439 | 0.65 | 0.78 | 47 | empty |
| 2 | 147 | 0.62 | 0.85 | 26 | empty |
| 3 | 294 | 0.61 | 0.79 | 42 | empty |
| 4 | 173 | 0.59 | 0.82 | 26 | empty |
| 5 | 127 | 0.56 | 0.83 | 26 | empty |
Interfaces
11 interfaces between chains.
- E–F · 2026 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 1937 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1802 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1767 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 727 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide (disulfide).
Compared structures
- 3E1I · Crystal Structure of BbetaD432A Variant Fibrinogen Fragment D with the Peptide Ligand… · the same entry in another collection · chain H against H, TM-score 1.00
- P02675 · AlphaFold monomer V2.0 prediction for fibrinogen beta chain (P02675) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P02679 · AlphaFold monomer V2.0 prediction for fibrinogen gamma chain (P02679) · a predicted model of the same protein · chain F against A, TM-score 0.99
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 P02671
- Every structure of UniProt P02675
- Every structure of UniProt P02679
- Elsewhere: RCSB PDB 3E1I · PDBe 3E1I · UniProt P02671 · UniProt P02675 · UniProt P02679
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