MolNFT v1 · #1765 · protein
The structure of residues 7-16 of the a alpha chain of human fibrinogen bound to bovine thrombin at 2.3 ångströms resolution
1BBR · Epsilon-thrombin: “The structure of residues 7-16 of the a alpha chain of human fibrinogen bound to bovine thrombin at 2.3…”. X-ray diffraction, 1 ligand (ACE), 11 pockets (best druggability 0.76). MolNFT v1 #1765 on GenesisL1: 3D…
- PDB
- 1BBR
- Type
- protein
- Length
- 915 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epsilon-thrombin; Fibrinogen ALPHA/ALPHA-E chain precursor
- EC
- 3.4.21.5
- UniProt
- P00735, P02671
- Ligands
- ACE
- Pockets
- 11 · best druggability 0.76
Structure
x-ray diffraction · 5 distinct chains · 14% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, J, M | Epsilon-thrombin (EC 3.4.21.5) | protein | 36 | 19% helix, 0% strand | P00735 |
| H | Epsilon-thrombin (EC 3.4.21.5) | protein | 150 | 11% helix, 37% strand | P00735 |
| E | Epsilon-thrombin (EC 3.4.21.5) | protein | 109 | 20% helix, 32% strand | P00735 |
| F, G, I | Fibrinogen ALPHA/ALPHA-E chain precursor | protein | 10 | 0% helix, 20% strand | P02671 |
| K, N | Epsilon-thrombin (EC 3.4.21.5) | protein | 259 | 12% helix, 35% strand | P00735 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 3 copies · chains H, F, K, G, N, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 885 | 0.76 | 0.80 | 67 | empty |
| 2 | 139 | 0.53 | 0.81 | 24 | empty |
| 3 | 230 | 0.52 | 0.76 | 39 | empty |
| 4 | 150 | 0.52 | 0.79 | 20 | empty |
| 5 | 146 | 0.51 | 0.79 | 26 | empty |
Interfaces
13 interfaces between chains.
- H–E · 3503 Ų buried · 60 hydrogen bonds · protein-protein
- J–K · 1385 Ų buried · 31 hydrogen bonds · protein-protein
- M–N · 1371 Ų buried · 29 hydrogen bonds · protein-protein
- L–H · 1108 Ų buried · 16 hydrogen bonds · protein-protein
- L–E · 738 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 3 covalent (disulfide, covalent ligand).
Compared structures
- 1BBR · The structure of residues 7-16 of the a alpha chain of human fibrinogen bound to bovine… · the same entry in another collection · chain I against I, TM-score 1.00
- P00735 · AlphaFold monomer V2.0 prediction for prothrombin (P00735) · a predicted model of the same protein · chain H against A, TM-score 0.97
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 P00735
- Every structure of UniProt P02671
- Elsewhere: RCSB PDB 1BBR · PDBe 1BBR · UniProt P00735 · UniProt P02671
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