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Crystal structure of murine siderocalin in complex with an Fab fragment

Analyse Crystal structure of murine siderocalin in complex with an Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3U9P
Type: protein
Length: 1,142 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Neutrophil gelatinase-associated lipocalin; Monoclonal Fab fragment heavy chain…
UniProt: P11672
Pockets: 10 · best druggability 0.59

Structure

x-ray diffraction · 6 distinct chains · 8% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Neutrophil gelatinase-associated lipocalin	protein	169	14% helix, 43% strand	P11672
D	Neutrophil gelatinase-associated lipocalin	protein	166	14% helix, 42% strand	P11672
H	Monoclonal Fab fragment heavy chain	protein	184	5% helix, 54% strand	—
K	Monoclonal Fab fragment heavy chain	protein	200	5% helix, 53% strand	—
L	Monoclonal Fab fragment light chain	protein	212	6% helix, 52% strand	—
M	Monoclonal Fab fragment light chain	protein	211	7% helix, 51% strand	—

Pockets

10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	429	0.59	0.75	50	empty
2	144	0.56	0.82	30	empty
3	323	0.55	0.75	36	empty
4	231	0.54	0.76	33	empty
5	224	0.53	0.76	40	empty

Interfaces

7 interfaces between chains.

K–M · 1631 Å² buried · 15 hydrogen bonds · protein-protein
H–L · 1588 Å² buried · 13 hydrogen bonds · protein-protein
D–L · 580 Å² buried · 16 hydrogen bonds · protein-protein
C–M · 576 Å² buried · 16 hydrogen bonds · protein-protein
L–M · 329 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

3U9P · Crystal Structure of Murine Siderocalin in Complex with an Fab Fragment · the same entry in another collection · chain K against K, TM-score 1.00
P11672 · AlphaFold monomer V2.0 prediction for neutrophil gelatinase- associated lipocalin (P11672) · a predicted model of the same protein · chain D against A, TM-score 0.98

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 P11672
Elsewhere: RCSB PDB 3U9P · PDBe 3U9P · UniProt P11672

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