Research workbench
Crystal structure of fragment double-D from human fibrin with two different bound ligands
Analyse Crystal structure of fragment double-D from human fibrin with two different… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FZC
- Type
- protein
- Length
- 1,382 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibrin
- UniProt
- P02671, P02675, P02679
- Ligands
- NAG, MAN, CA
- Pockets
- 19 · best druggability 0.69
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Fibrin | protein | 74 | 74% helix, 1% strand | P02671 |
| B, E | Fibrin | protein | 308 | 24% helix, 24% strand | P02675 |
| C, F | Fibrin | protein | 301 | 23% helix, 24% strand | P02679 |
| G, H | Fibrin | protein | 4 | 0% helix, 25% strand | — |
| I, J | Fibrin | protein | 4 | 0% helix, 25% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, I, E, J
- MAN · alpha-D-mannopyranose · sugar
- CA · Calcium ion · metal · 4 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 478 | 0.69 | 0.80 | 64 | empty |
| 2 | 207 | 0.60 | 0.81 | 33 | empty |
| 3 | 220 | 0.59 | 0.80 | 35 | empty |
| 4 | 130 | 0.58 | 0.84 | 26 | empty |
| 5 | 140 | 0.56 | 0.82 | 26 | empty |
Interfaces
11 interfaces between chains.
- E–F · 2305 Ų buried · 26 hydrogen bonds · protein-protein
- B–C · 2272 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 2015 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2001 Ų buried · 27 hydrogen bonds · protein-protein
- D–F · 974 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 1FZC · Crystal structure of fragment double-D from human fibrin with two different bound ligands · the same entry in another collection · chain J against J, TM-score 1.00
- P02675 · AlphaFold monomer V2.0 prediction for fibrinogen beta chain (P02675) · a predicted model of the same protein · chain E 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 1FZC · PDBe 1FZC · UniProt P02671 · UniProt P02675 · UniProt P02679
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