Research workbench
X-ray crystal structure of DUF2500 (PF10694) from klebsiella pneumoniae, northeast structural genomics consortium target KPR96
Analyse X-ray crystal structure of DUF2500 (PF10694) from klebsiella pneumoniae… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q6C
- Type
- protein
- Length
- 1,067 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable receptor yhhm
- UniProt
- D3RD65
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 9 distinct chains · 9% helix, 63% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable receptor yhhm | protein | 66 | 9% helix, 64% strand | D3RD65 |
| B, C, D, F, G, H, L, M | Probable receptor yhhm | protein | 67 | 9% helix, 63% strand | D3RD65 |
| E | Probable receptor yhhm | protein | 64 | 9% helix, 66% strand | D3RD65 |
| I | Probable receptor yhhm | protein | 71 | 8% helix, 62% strand | D3RD65 |
| J | Probable receptor yhhm | protein | 64 | 9% helix, 56% strand | D3RD65 |
| K | Probable receptor yhhm | protein | 65 | 9% helix, 65% strand | D3RD65 |
| N | Probable receptor yhhm | protein | 66 | 9% helix, 64% strand | D3RD65 |
| O | Probable receptor yhhm | protein | 70 | 9% helix, 63% strand | D3RD65 |
| P | Probable receptor yhhm | protein | 65 | 9% helix, 62% strand | D3RD65 |
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 818 | 0.77 | 0.81 | 76 | empty |
| 2 | 407 | 0.77 | 0.86 | 50 | empty |
| 3 | 888 | 0.76 | 0.80 | 79 | empty |
| 4 | 232 | 0.56 | 0.78 | 35 | empty |
| 5 | 371 | 0.56 | 0.75 | 38 | empty |
Interfaces
24 interfaces between chains.
- A–D · 549 Ų buried · 6 hydrogen bonds · protein-protein
- C–F · 499 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 495 Ų buried · 9 hydrogen bonds · protein-protein
- L–M · 495 Ų buried · 7 hydrogen bonds · protein-protein
- K–N · 491 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 3Q6C · X-ray crystal structure of duf2500 (pf10694) from klebsiella pneumoniae, northeast… · 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
- Every structure of UniProt D3RD65
- Elsewhere: RCSB PDB 3Q6C · PDBe 3Q6C · UniProt D3RD65
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