MolNFT v1 · #51353 · protein
Crystal structure of a sparc-collagen complex
2V53: “Crystal structure of a sparc-collagen complex”. X-ray diffraction, 3 ligands (NAG, CA, SO4), 2 pockets (best druggability 0.62). MolNFT v1 #51353 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2V53
- Type
- protein
- Length
- 313 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sparc; Collagen alpha-1(III) chain
- UniProt
- P09486, P02461
- Ligands
- NAG, CA, SO4
- Pockets
- 2 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sparc | protein | 214 | 37% helix, 9% strand | P09486 |
| B, C, D | Collagen alpha-1(III) chain | protein | 33 | 0% helix, 3% strand | P02461 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- CA · Calcium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 508 | 0.62 | 0.75 | 45 | empty |
| 2 | 72 | 0.35 | 0.75 | 13 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1052 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1010 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 947 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 525 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 269 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified, 7 disulfide, 1 glycan (hydroxylation, disulfide, N-glycosylation).
Compared structures
- 2V53 · Crystal structure of a SPARC-collagen complex · the same entry in another collection · chain D against D, TM-score 1.00
- P09486 · AlphaFold monomer V2.0 prediction for sparc (P09486) · a predicted model of the same protein · chain A against A, TM-score 0.74
- P02461 · AlphaFold monomer V2.0 prediction for collagen alpha-1(III) chain (P02461) · a predicted model of the same protein · chain B against A, TM-score 0.47
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 P09486
- Every structure of UniProt P02461
- Elsewhere: RCSB PDB 2V53 · PDBe 2V53 · UniProt P09486 · UniProt P02461
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