Research workbench
Crystal structure of fragment D-dimer from human fibrin complexed with gly-hydroxypro-arg-pro-amide
Analyse Crystal structure of fragment D-dimer from human fibrin complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2HLO
- Type
- protein
- Length
- 1,305 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibrin alpha chain; Fibrin beta chain; Fibrin, gamma polypeptide; Gly-hyp-arg-pro-amide…
- UniProt
- P02671, P02675, Q53Y18
- Ligands
- NAG, NDG, CA, NH2
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 7 distinct chains · 25% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fibrin alpha chain | protein | 67 | 72% helix, 1% strand | P02671 |
| B | Fibrin beta chain | protein | 303 | 19% helix, 26% strand | P02675 |
| C | Fibrin, gamma polypeptide | protein | 292 | 23% helix, 25% strand | Q53Y18 |
| D | Fibrin alpha chain | protein | 54 | 57% helix, 2% strand | P02671 |
| E | Fibrin beta chain | protein | 296 | 21% helix, 27% strand | P02675 |
| F | Fibrin, gamma polypeptide | protein | 285 | 21% helix, 27% strand | Q53Y18 |
| G, H | Gly-hyp-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, E
- NDG · 2-acetamido-2-deoxy-alpha-D-glucopyranose · sugar
- CA · Calcium ion · metal · 7 copies · chains B, C, E, F
- NH2 · Amino group · ion · 2 copies · chains C, G, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 264 | 0.68 | 0.84 | 36 | empty |
| 2 | 174 | 0.62 | 0.84 | 27 | empty |
| 3 | 179 | 0.62 | 0.83 | 26 | empty |
| 4 | 328 | 0.57 | 0.76 | 42 | empty |
| 5 | 241 | 0.55 | 0.77 | 30 | empty |
Interfaces
9 interfaces between chains.
- B–C · 2096 Ų buried · 22 hydrogen bonds · protein-protein
- E–F · 1932 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1901 Ų buried · 24 hydrogen bonds · protein-protein
- D–E · 1740 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 891 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 2 glycan, 2 modified (disulfide, N-glycosylation, hydroxylation).
Compared structures
- 2HLO · Crystal Structure of Fragment D-dimer from Human Fibrin Complexed with… · the same entry in another collection · chain E against E, 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
- P02671 · AlphaFold monomer V2.0 prediction for fibrinogen alpha chain (P02671) · a predicted model of the same protein · chain D against A, TM-score 0.85
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 2HLO · PDBe 2HLO · UniProt P02671 · UniProt P02675 · UniProt Q53Y18
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