MolNFT v1 · #103197 · protein
CA2+-stabilized adhesin helps an antarctic bacterium reach out and bind ice
4P99 · MPAFP_RII tetra-tandemer: “CA2+-stabilized adhesin helps an antarctic bacterium reach out and bind ice”. X-ray diffraction, 1 ligand (CA), 12 pockets (best druggability 0.53). MolNFT v1 #103197 on GenesisL1: 3D structure, binding…
- PDB
- 4P99
- Type
- protein
- Length
- 1,660 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MPAFP_RII tetra-tandemer
- Ligands
- CA
- Pockets
- 12 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | MPAFP_RII tetra-tandemer | protein | 415 | 10% helix, 52% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 104 copies · chains A, C, B, D
- EDO · 1,2-ethanediol · additive · 44 copies · chains A, D, C, B
- BOG · octyl beta-D-glucopyranoside · additive · 3 copies · chains B, C, D
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 357 | 0.53 | 0.74 | 47 | CA, EDO |
| 2 | 206 | 0.50 | 0.77 | 27 | empty |
| 3 | 208 | 0.42 | 0.72 | 42 | empty |
| 4 | 153 | 0.41 | 0.74 | 30 | CA |
| 5 | 121 | 0.38 | 0.75 | 20 | CA |
Interfaces
5 interfaces between chains.
- B–C · 772 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 660 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 562 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 396 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 49 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4P99 · Ca2+-stabilized adhesin helps an Antarctic bacterium reach out and bind ice · the same entry in another collection · chain A 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
- Elsewhere: RCSB PDB 4P99 · PDBe 4P99
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