SMTL ID : 6ifg.1 (1 other biounit)

Crystal structure of M1 zinc metallopeptidase E323A mutant bound to Tyr-ser-ala substrate from Deinococcus radiodurans

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x TYR- SER- ALA: Tripeptides (TYR-SER-ALA)(Non-covalent)

TYR-SER-ALA.1: 16 residues within 4Å: Chain A: L.165, E.167, L.302, A.303, L.304, E.305, S.316, R.318, V.321, H.324, H.328, E.347, F.393, Y.398 Ligands: ZN.2, FMT.5 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:E.167, A:L.302, A:L.302, A:L.302, A:L.304 Hydrogen bonds: A:E.167, A:E.167, A:E.167, A:A.303, A:A.303, A:S.316 Water bridges: A:E.305 Salt bridges: A:R.318 pi-Stacking: A:F.393

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.324, H.328, E.347, Y.398 Ligands: TYR-SER-ALA.1 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.324, A:H.328, A:E.347, A:E.347 ZN.3: 5 residues within 4Å: Chain A: D.54, V.55, D.183, P.184 Ligands: FMT.4 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.54, A:V.55, A:D.183, A:P.184, H2O.5

7 x FMT: FORMIC ACID(Non-functional Binders)

FMT.4: 7 residues within 4Å: Chain A: D.54, R.83, S.182, D.183, P.184 Ligands: ZN.3, FMT.6 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.183 Water bridges: A:V.55, A:P.184 FMT.5: 3 residues within 4Å: Chain A: E.354, F.399 Ligands: TYR-SER-ALA.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.354 FMT.6: 5 residues within 4Å: Chain A: G.52, L.53, D.54, R.83 Ligands: FMT.4 2 PLIP interactions: 2 interactions with chain A Water bridges: A:G.52, A:L.53 FMT.7: 4 residues within 4Å: Chain A: L.143, W.155, Q.156, N.157 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.156, A:N.157 FMT.8: 3 residues within 4Å: Chain A: V.40, S.182, A.338 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.182 FMT.9: 8 residues within 4Å: Chain A: A.199, A.200, F.205, L.217, F.219, L.237, R.239, I.257 No protein-ligand interaction detected (PLIP) FMT.10: 5 residues within 4Å: Chain A: F.393, D.394, A.395, Y.398, F.399 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Agrawal, R. et al., Two-domain aminopeptidase of M1 family: Structural features for substrate binding and gating in absence of C-terminal domain. J.Struct.Biol. (2019)

Release Date

2019-09-25

Peptides

Zinc metalloprotease: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Zinc metalloprotease

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