MolNFT v1 · #120657 · protein
Crystal structure of the ygjg-protein a-ZPA963-calmodulin complex
5H7D · Putrescine AMINOTRANSFERASE,IMMUNOGLOBULIN G-binding…: “Crystal structure of the ygjg-protein a-ZPA963-calmodulin complex”. X-ray diffraction, 1 ligand (CA), 20 pockets (best druggability 0.87). MolNFT v1 #120657 on GenesisL1: 3D…
- PDB
- 5H7D
- Type
- protein
- Length
- 4,860 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putrescine AMINOTRANSFERASE,IMMUNOGLOBULIN G-binding protein a; ZPA963,CALMODULIN
- EC
- 2.6.1.82
- UniProt
- P42588, P38507, O16305
- Ligands
- CA
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 3 distinct chains · 57% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, I, J, M, N | Putrescine AMINOTRANSFERASE,IMMUNOGLOBULIN G-binding protein a (EC 2.6.1.82) | protein | 495 | 52% helix, 16% strand | P42588, P38507 |
| E, G, K, O | ZPA963,CALMODULIN | protein | 113 | 71% helix, 2% strand | O16305 |
| F, H, L, P | ZPA963,CALMODULIN | protein | 112 | 65% helix, 2% strand | O16305 |
Ligands and binding sites
- CA · Calcium ion · metal · 16 copies · chains E, F, G, H, K, L, O, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1179 | 0.87 | 0.88 | 121 | empty |
| 2 | 1136 | 0.85 | 0.86 | 103 | empty |
| 3 | 501 | 0.84 | 0.90 | 78 | empty |
| 4 | 489 | 0.84 | 0.90 | 74 | empty |
| 5 | 478 | 0.84 | 0.90 | 62 | empty |
Interfaces
17 interfaces between chains.
- I–J · 6397 Ų buried · 62 hydrogen bonds · protein-protein
- M–N · 6389 Ų buried · 63 hydrogen bonds · protein-protein
- C–D · 6384 Ų buried · 58 hydrogen bonds · protein-protein
- A–B · 6383 Ų buried · 60 hydrogen bonds · protein-protein
- J–M · 845 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 5H7D · Crystal structure of the YgjG-protein A-Zpa963-calmodulin complex · the same entry in another collection · chain K against K, 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 P42588
- Every structure of UniProt P38507
- Every structure of UniProt O16305
- Elsewhere: RCSB PDB 5H7D · PDBe 5H7D · UniProt P42588 · UniProt P38507 · UniProt O16305
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