MolNFT v1 · #38625 · protein
Crystal structure of human fragment D complexed with ala-his-arg-pro- amide
2H43 · Fibrinogen alpha chain: “Crystal structure of human fragment D complexed with ala-his-arg-pro- amide”. X-ray diffraction, 4 ligands (NAG, NDG, CA), 20 pockets (best druggability 0.72). MolNFT v1 #38625 on GenesisL1: 3D structure…
- PDB
- 2H43
- Type
- protein
- Length
- 1,332 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, NDG, CA, NH2
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Fibrinogen alpha chain | protein | 70 | 63% helix, 1% strand | P02671 |
| B, E | Fibrinogen beta chain | protein | 302 | 22% helix, 25% strand | P02675 |
| C, F | Fibrinogen gamma chain | protein | 290 | 22% helix, 25% strand | P02679 |
| I, J | Gly-his-arg-pro-amide peptide ligand | protein | 4 | 0% helix, 25% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains B, I, E, J
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar · chains J
- CA · Calcium ion · metal · 6 copies · chains B, C, E, F
- NH2 · Amino group · ion · 2 copies · chains B, I, E, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 606 | 0.72 | 0.80 | 64 | empty |
| 2 | 167 | 0.62 | 0.84 | 25 | empty |
| 3 | 158 | 0.62 | 0.84 | 26 | empty |
| 4 | 203 | 0.60 | 0.82 | 38 | CA |
| 5 | 206 | 0.56 | 0.79 | 35 | CA |
Interfaces
9 interfaces between chains.
- E–F · 2131 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 2069 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1914 Ų buried · 23 hydrogen bonds · protein-protein
- D–E · 1906 Ų buried · 23 hydrogen bonds · protein-protein
- D–F · 846 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2H43 · Crystal Structure of Human Fragment D Complexed with Ala-His-Arg-Pro-amide · 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
- P02679 · AlphaFold monomer V2.0 prediction for fibrinogen gamma chain (P02679) · a predicted model of the same protein · chain F against A, TM-score 0.98
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 2H43 · PDBe 2H43 · UniProt P02671 · UniProt P02675 · UniProt P02679
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