SMTL ID : 8ccr.1

Crystal structure of the T19D mutant of the de novo diheme binding 4D2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

2 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 21 residues within 4Å: Chain A: R.6, H.9, R.10, A.13, V.44, Y.45, G.48, Q.49, M.51, L.52, H.67, R.68, A.71, V.102, Y.103, G.106, Q.107, M.109, L.110 Ligands: LMR.2, HEM.3 19 PLIP interactions: 19 interactions with chain A, Hydrophobic interactions: A:R.6, A:R.10, A:V.44, A:V.44, A:Y.45, A:L.52, A:R.68, A:A.71, A:V.102, A:Y.103 Salt bridges: A:R.6 pi-Stacking: A:H.9, A:H.9, A:H.9, A:H.67, A:H.67, A:H.67 Metal complexes: A:H.9, A:H.67 HEM.3: 22 residues within 4Å: Chain A: V.16, Y.17, G.20, Q.21, M.23, L.24, N.29, R.34, H.37, R.38, A.41, V.74, G.78, Q.79, M.81, L.82, N.87, R.92, H.95, A.99, Y.103 Ligands: HEM.1 20 PLIP interactions: 20 interactions with chain A, Hydrophobic interactions: A:V.16, A:Y.17, A:Q.21, A:M.23, A:L.24, A:L.24, A:R.38, A:A.41, A:L.82, A:A.99, A:Y.103 Hydrogen bonds: A:N.29, A:N.87, A:N.87 Salt bridges: A:R.34, A:R.34, A:R.92 pi-Stacking: A:H.95 Metal complexes: A:H.37, A:H.95

1 x LMR: (2S)-2-hydroxybutanedioic acid(Non-covalent)

LMR.2: 3 residues within 4Å: Chain A: G.1, R.6 Ligands: HEM.1 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.6

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.4: 3 residues within 4Å: Chain A: N.84, T.85, S.86 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hutchins, G.H. et al., An expandable, modular de novo protein platform for precision redox engineering. Proc.Natl.Acad.Sci.USA (2023)

Release Date

2023-08-09

Peptides

4D2 (mutant T19D): A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

4D2 (mutant T19D)