MolNFT v1 · #151065 · protein

Klebsiella pneumoniae type II secretion system outer membrane complex. puld, puls and pulc hr domain.

6HCG · Type II secretion system protein D: “Klebsiella pneumoniae type II secretion system outer membrane complex. puld, puls and pulc hr domain.”. Electron microscopy, 20 pockets (best druggability 0.82). MolNFT v1 #151065 on GenesisL1…

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.

Pocket	Volume (Å³)	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 Å² buried · 76 hydrogen bonds · protein-protein
M–N · 6496 Å² buried · 78 hydrogen bonds · protein-protein
I–J · 6472 Å² buried · 75 hydrogen bonds · protein-protein
B–C · 6461 Å² buried · 76 hydrogen bonds · protein-protein
C–D · 6460 Å² 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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