Research workbench
Crystal structure of fragment D from lamprey fibrinogen complexed with the peptide gly-his-arg-pro-amide
Analyse Crystal structure of fragment D from lamprey fibrinogen complexed with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LWU
- Type
- protein
- Length
- 2,932 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibrinogen alpha-1 chain; Fibrinogen beta chain; Fibrinogen gamma chain; Peptide ligand…
- UniProt
- P02674, P02678, P04115
- Ligands
- MAN, NAG, NDG, BMA, GAL, CA, NH2
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 31% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, G, J | Fibrinogen alpha-1 chain | protein | 99 | 70% helix, 1% strand | P02674 |
| B, E, H, K | Fibrinogen beta chain | protein | 315 | 28% helix, 23% strand | P02678 |
| C, F | Fibrinogen gamma chain | protein | 317 | 28% helix, 22% strand | P04115 |
| I, L | Fibrinogen gamma chain | protein | 313 | 26% helix, 22% strand | P04115 |
| M, N, O, P | Peptide ligand gly-his-arg-pro-NH2 | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 10 copies · chains H
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains L, C, E, N, F, I
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · 9 copies · chains B, M, H, O, K, P
- BMA · beta-D-mannopyranose · sugar · 2 copies
- GAL · beta-D-galactopyranose · sugar · chains H
- CA · Calcium ion · metal · 8 copies · chains B, C, E, F, H, I, K, L
- NH2 · Amino group · ion · 4 copies · chains B, M, E, N, H, O, K, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 85 | 0.72 | 0.95 | 23 | empty |
| 2 | 205 | 0.69 | 0.86 | 26 | empty |
| 3 | 202 | 0.69 | 0.86 | 27 | empty |
| 4 | 194 | 0.68 | 0.86 | 26 | empty |
| 5 | 207 | 0.67 | 0.85 | 27 | empty |
Interfaces
30 interfaces between chains.
- H–I · 2477 Ų buried · 27 hydrogen bonds · protein-protein
- K–L · 2469 Ų buried · 27 hydrogen bonds · protein-protein
- D–E · 2418 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2417 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 2386 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 1LWU · Crystal structure of fragment D from lamprey fibrinogen complexed with the peptide… · the same entry in another collection · chain P against P, 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 P02674
- Every structure of UniProt P02678
- Every structure of UniProt P04115
- Elsewhere: RCSB PDB 1LWU · PDBe 1LWU · UniProt P02674 · UniProt P02678 · UniProt P04115
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.