Research workbench
Crystal structure of D-dimer from human fibrin complexed with gly-his- arg-pro-tyr-amide
Analyse Crystal structure of D-dimer from human fibrin complexed with gly-his… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Z4E
- Type
- protein
- Length
- 1,315 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibrinogen alpha chain; Fibrinogen beta chain; Fibrinogen, gamma polypeptide; Fibrin B…
- UniProt
- P02671, P02675, Q53Y18
- Ligands
- NAG, CA
- Pockets
- 16 · best druggability 0.72
Structure
x-ray diffraction · 8 distinct chains · 25% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fibrinogen alpha chain | protein | 67 | 67% helix, 1% strand | P02671 |
| B | Fibrinogen beta chain | protein | 303 | 21% helix, 27% strand | P02675 |
| C | Fibrinogen, gamma polypeptide | protein | 292 | 22% helix, 27% strand | Q53Y18 |
| D | Fibrinogen alpha chain | protein | 54 | 65% helix, 2% strand | P02671 |
| E | Fibrinogen beta chain | protein | 296 | 22% helix, 27% strand | P02675 |
| F | Fibrinogen, gamma polypeptide | protein | 285 | 20% helix, 28% strand | Q53Y18 |
| S, T | Fibrin B knob (tetrapeptide) | protein | 4 | 0% helix, 25% strand | — |
| I, J | Fibrin B knob (pentapeptide) | protein | 5 | 0% helix, 20% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains B, I, E, J
- CA · Calcium ion · metal · 8 copies · chains B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 623 | 0.72 | 0.79 | 65 | empty |
| 2 | 181 | 0.62 | 0.83 | 26 | empty |
| 3 | 156 | 0.61 | 0.84 | 25 | empty |
| 4 | 207 | 0.59 | 0.80 | 36 | CA |
| 5 | 120 | 0.57 | 0.84 | 24 | CA |
Interfaces
11 interfaces between chains.
- B–C · 1982 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1875 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1831 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 1709 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 825 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 2Z4E · Crystal Structure of D-Dimer from Human Fibrin Complexed with Gly-His-Arg-Pro-Tyr-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 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 P02671
- Every structure of UniProt P02675
- Every structure of UniProt Q53Y18
- Elsewhere: RCSB PDB 2Z4E · PDBe 2Z4E · UniProt P02671 · UniProt P02675 · UniProt Q53Y18
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