MolNFT v1 · #132612 · protein

Crystal structure of gamma-chymotrypsin at pH 5.6, cryo temperature

5R49: “Crystal structure of gamma-chymotrypsin at pH 5.6, cryo temperature”. X-ray diffraction, 1 ligand (IOD). MolNFT v1 #132612 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5R49
Type: protein
Length: 247 residues
Chains: 5
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Gamma-chymotrypsin; Peptide swpw; Peptide tpgvy
EC: 3.4.21.1
UniProt: P00766
Ligands: IOD

Structure

x-ray diffraction · 5 distinct chains · 11% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Gamma-chymotrypsin (EC 3.4.21.1)	protein	10	0% helix, 0% strand	P00766
B	Gamma-chymotrypsin (EC 3.4.21.1)	protein	131	2% helix, 40% strand	P00766
C	Gamma-chymotrypsin (EC 3.4.21.1)	protein	97	25% helix, 40% strand	P00766
D	Peptide swpw	protein	4	0% helix, 50% strand	—
E	Peptide tpgvy	protein	5	0% helix, 60% strand	—

Ligands and binding sites

IOD · Iodide ion · ion · chains B
MLI · Malonate ion · additive · chains A, B

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

Interfaces

8 interfaces between chains.

B–C · 3033 Å² buried · 46 hydrogen bonds · protein-protein
A–B · 493 Å² buried · 2 hydrogen bonds · protein-protein
C–E · 401 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 374 Å² buried · 9 hydrogen bonds · protein-protein
D–E · 297 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

5R49 · Crystal Structure of gamma-Chymotrypsin at pH 5.6, cryo temperature · the same entry in another collection · chain E against E, TM-score 1.00
P00766 · AlphaFold monomer V2.0 prediction for chymotrypsinogen a (P00766) · a predicted model of the same protein · chain C 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 P00766
Elsewhere: RCSB PDB 5R49 · PDBe 5R49 · UniProt P00766

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