MolNFT v1 · #160714 · protein
Complex of CRACR2A with a dynein light intermediate chain peptide
6PSD · Ef-hand calcium-binding domain-containing protein 4B: “Complex of CRACR2A with a dynein light intermediate chain peptide”. X-ray diffraction, 1 ligand (CA), 7 pockets (best druggability 0.66). MolNFT v1 #160714 on GenesisL1: 3D…
- PDB
- 6PSD
- Type
- protein
- Length
- 691 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ef-hand calcium-binding domain-containing protein 4B; Cdna FLJ10219 fis, clone…
- UniProt
- Q9BSW2, B3KM42
- Ligands
- CA
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 11 distinct chains · 67% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, A, K | Ef-hand calcium-binding domain-containing protein 4B | protein | 73 | 62% helix, 5% strand | Q9BSW2 |
| C, M | Ef-hand calcium-binding domain-containing protein 4B | protein | 72 | 63% helix, 3% strand | Q9BSW2 |
| G | Ef-hand calcium-binding domain-containing protein 4B | protein | 71 | 63% helix, 3% strand | Q9BSW2 |
| I | Ef-hand calcium-binding domain-containing protein 4B | protein | 73 | 66% helix, 3% strand | Q9BSW2 |
| O | Ef-hand calcium-binding domain-containing protein 4B | protein | 72 | 64% helix, 3% strand | Q9BSW2 |
| F, P | Cdna FLJ10219 fis, clone HEMBA1007018, highly similar to cytoplasmic dynein 1 light intermediate chain 1 | protein | 13 | 77% helix, 0% strand | B3KM42 |
| D, L | Cdna FLJ10219 fis, clone HEMBA1007018, highly similar to cytoplasmic dynein 1 light intermediate chain 1 | protein | 15 | 87% helix, 0% strand | B3KM42 |
| B | Cdna FLJ10219 fis, clone HEMBA1007018, highly similar to cytoplasmic dynein 1 light intermediate chain 1 | protein | 13 | 69% helix, 0% strand | B3KM42 |
| H | Cdna FLJ10219 fis, clone HEMBA1007018, highly similar to cytoplasmic dynein 1 light intermediate chain 1 | protein | 14 | 86% helix, 0% strand | B3KM42 |
| J | Cdna FLJ10219 fis, clone HEMBA1007018, highly similar to cytoplasmic dynein 1 light intermediate chain 1 | protein | 15 | 87% helix, 0% strand | B3KM42 |
| N | Cdna FLJ10219 fis, clone HEMBA1007018, highly similar to cytoplasmic dynein 1 light intermediate chain 1 | protein | 14 | 79% helix, 0% strand | B3KM42 |
Ligands and binding sites
- CA · Calcium ion · metal · 8 copies · chains E, C, A, G, I, K, M, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 547 | 0.66 | 0.77 | 63 | empty |
| 2 | 129 | 0.43 | 0.76 | 23 | empty |
| 3 | 131 | 0.40 | 0.74 | 31 | empty |
| 4 | 112 | 0.37 | 0.74 | 18 | empty |
| 5 | 97 | 0.37 | 0.75 | 17 | empty |
Interfaces
30 interfaces between chains.
- C–D · 681 Ų buried · 0 hydrogen bonds · protein-protein
- K–L · 619 Ų buried · 0 hydrogen bonds · protein-protein
- M–N · 609 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 608 Ų buried · 0 hydrogen bonds · protein-protein
- E–F · 607 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6PSD · Complex of CRACR2a with a Dynein Light Intermediate Chain Peptide · the same entry in another collection · chain P against P, 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 Q9BSW2
- Every structure of UniProt B3KM42
- Elsewhere: RCSB PDB 6PSD · PDBe 6PSD · UniProt Q9BSW2 · UniProt B3KM42
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