MolNFT v1 · #86417 · protein
Structure of RFNBPA(189-505) in complex with fibrinogen gamma chain C-terminal peptide
4B60 · Fibronectin-binding protein a: “Structure of RFNBPA(189-505) in complex with fibrinogen gamma chain C-terminal peptide”. X-ray diffraction, 1 ligand (CA), 8 pockets (best druggability 0.75). MolNFT v1 #86417 on GenesisL1: 3D…
- PDB
- 4B60
- Type
- protein
- Length
- 618 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibronectin-binding protein a; Fibrinogen gamma chain
- UniProt
- P14738, P02679
- Ligands
- CA
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fibronectin-binding protein a | protein | 299 | 5% helix, 54% strand | P14738 |
| B | Fibronectin-binding protein a | protein | 293 | 6% helix, 52% strand | P14738 |
| C | Fibrinogen gamma chain | protein | 14 | 0% helix, 79% strand | P02679 |
| D | Fibrinogen gamma chain | protein | 12 | 0% helix, 75% strand | P02679 |
Ligands and binding sites
- CA · Calcium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1040 | 0.75 | 0.78 | 109 | empty |
| 2 | 221 | 0.64 | 0.83 | 40 | empty |
| 3 | 176 | 0.60 | 0.82 | 29 | empty |
| 4 | 66 | 0.43 | 0.81 | 12 | empty |
| 5 | 82 | 0.41 | 0.79 | 14 | empty |
Interfaces
4 interfaces between chains.
- A–C · 957 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 923 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 482 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 38 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4B60 · Structure of rFnBPA(189-505) in complex with fibrinogen gamma chain C- terminal peptide · the same entry in another collection · chain D against D, TM-score 1.00
- P14738 · AlphaFold monomer V2.0 prediction for fibronectin-binding protein a (P14738) · a predicted model of the same protein · chain A 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 D against A, TM-score 0.41
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 P14738
- Every structure of UniProt P02679
- Elsewhere: RCSB PDB 4B60 · PDBe 4B60 · UniProt P14738 · UniProt P02679
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