Research workbench
Klebsiella pneumoniae type II secretion system outer membrane complex. puld, puls and pulc hr domain.
Analyse Klebsiella pneumoniae type II secretion system outer membrane complex. puld… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HCG
- Type
- protein
- Length
- 11,295 residues
- Chains
- 45
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type II secretion system protein D; Pullulanase; Pectic enzymes secretion protein outc
- UniProt
- A0A0J2GHI1, A0A060VDD0
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L, M, N, O | Type II secretion system protein D | protein | 592 | 24% helix, 30% strand | A0A0J2GHI1 |
| P, Q, R, S, T, U, V, W, X, Y, Z, a, b, c, d | Pullulanase | protein | 93 | 74% helix, 0% strand | — |
| e, f, g, h, i, j, k, l, m, n, o, p, q, r, s | Pectic enzymes secretion protein outc | protein | 68 | 0% helix, 47% strand | A0A060VDD0 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 516 | 0.82 | 0.88 | 85 | empty |
| 2 | 704 | 0.80 | 0.85 | 86 | empty |
| 3 | 618 | 0.80 | 0.85 | 94 | empty |
| 4 | 1084 | 0.80 | 0.82 | 120 | empty |
| 5 | 437 | 0.80 | 0.88 | 77 | empty |
Interfaces
90 interfaces between chains.
- G–H · 6503 Ų buried · 76 hydrogen bonds · protein-protein
- M–N · 6496 Ų buried · 78 hydrogen bonds · protein-protein
- I–J · 6472 Ų buried · 75 hydrogen bonds · protein-protein
- B–C · 6461 Ų buried · 76 hydrogen bonds · protein-protein
- C–D · 6460 Ų buried · 74 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 6HCG · Klebsiella pneumoniae type II secretion system outer membrane complex. PulD, PulS and… · the same entry in another collection · chain B against B, 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 A0A0J2GHI1
- Every structure of UniProt A0A060VDD0
- Elsewhere: RCSB PDB 6HCG · PDBe 6HCG · UniProt A0A0J2GHI1 · UniProt A0A060VDD0
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