MolNFT v1 · #79766 · protein
Crystal structure of ompa-like domain from acinetobacter baumannii in complex with L-ala-gamma-D-glu-M-dap-D-ala-D-ala
3TD5 · Outer membrane protein OMP38: “Crystal structure of ompa-like domain from acinetobacter baumannii in complex with…”. X-ray diffraction, 2 ligands (API, CL), 10 pockets (best druggability 0.52). MolNFT v1 #79766 on GenesisL1: 3D…
- PDB
- 3TD5
- Type
- protein
- Length
- 994 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Outer membrane protein OMP38; PEPTIDE(L-ala-gamma-D-glu-M-dap-D-ala-D-ala)
- UniProt
- Q6RYW5
- Ligands
- API, CL
- Pockets
- 10 · best druggability 0.52
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Outer membrane protein OMP38 | protein | 119 | 40% helix, 27% strand | Q6RYW5 |
| B, E, F | Outer membrane protein OMP38 | protein | 121 | 40% helix, 28% strand | Q6RYW5 |
| C, D, G, H | Outer membrane protein OMP38 | protein | 120 | 40% helix, 28% strand | Q6RYW5 |
| I, J, K, L, M, N, O, P | PEPTIDE(L-ala-gamma-D-glu-M-dap-D-ala-D-ala) | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- API · 2,6-diaminopimelic acid · ligand · 8 copies · chains A, I, B, J, C, K, D, L, E, M, F, N, G, O, H, P
- CL · Chloride ion · ion · 6 copies · chains A, B, C, F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 231 | 0.52 | 0.76 | 22 | empty |
| 2 | 169 | 0.46 | 0.76 | 26 | empty |
| 3 | 157 | 0.46 | 0.77 | 26 | empty |
| 4 | 133 | 0.46 | 0.78 | 21 | empty |
| 5 | 56 | 0.39 | 0.80 | 12 | empty |
Interfaces
16 interfaces between chains.
- E–F · 845 Ų buried · 21 hydrogen bonds · protein-protein
- G–H · 786 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 784 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 717 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 630 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 covalent, 16 d-amino, 8 modified (covalent ligand, D-amino acid, nonstandard).
Compared structures
- 3TD5 · Crystal structure of OmpA-like domain from Acinetobacter baumannii in complex with… · 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 Q6RYW5
- Elsewhere: RCSB PDB 3TD5 · PDBe 3TD5 · UniProt Q6RYW5
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