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Crystal structure of the second and third fibronectin F1 modules in complex with a fragment of staphylococcus aureus fnbpa-1

Analyse Crystal structure of the second and third fibronectin F1 modules in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2RKZ
Type: protein
Length: 641 residues
Chains: 12
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fibronectin; Peptide from fibronectin-binding protein a
UniProt: P02751, P14738
Ligands: ACE, NH2
Pockets: 4 · best druggability 0.76

Structure

x-ray diffraction · 8 distinct chains · 0% helix, 58% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, F	Fibronectin	protein	89	0% helix, 62% strand	P02751
C	Fibronectin	protein	90	0% helix, 61% strand	P02751
D	Fibronectin	protein	86	0% helix, 66% strand	P02751
E	Fibronectin	protein	81	0% helix, 62% strand	P02751
M	Peptide from fibronectin-binding protein a	protein	18	0% helix, 39% strand	P14738
N, R	Peptide from fibronectin-binding protein a	protein	19	0% helix, 37% strand	P14738
O, Q	Peptide from fibronectin-binding protein a	protein	20	0% helix, 40% strand	P14738
P	Peptide from fibronectin-binding protein a	protein	21	0% helix, 38% strand	P14738

Ligands and binding sites

ACE · Acetyl group · ligand · chains A, B, M
NH2 · Amino group · ion · chains O, P
SIN · Succinic acid · additive · 3 copies · chains A, M, B, N, C, O

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1200	0.76	0.79	127	NH2
2	551	0.74	0.82	98	empty
3	232	0.64	0.82	32	empty
4	151	0.61	0.84	30	empty

Interfaces

41 interfaces between chains.

B–N · 1049 Å² buried · 26 hydrogen bonds · protein-protein
F–R · 1024 Å² buried · 26 hydrogen bonds · protein-protein
C–O · 1018 Å² buried · 25 hydrogen bonds · protein-protein
D–P · 990 Å² buried · 23 hydrogen bonds · protein-protein
E–Q · 964 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

2RKZ · Crystal structure of the second and third fibronectin f1 modules in complex with a… · the same entry in another collection · chain R against R, 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 P02751
Every structure of UniProt P14738
Elsewhere: RCSB PDB 2RKZ · PDBe 2RKZ · UniProt P02751 · UniProt P14738

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