SMTL ID : 5l7f.1 (1 other biounit)

Crystal structure of MMP12 mutant K421A in complex with RXP470.1 conjugated with fluorophore Cy5,5 in space group P21.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.114, H.118, H.124 Ligands: R47.9 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.114, A:H.118, A:H.124 ZN.2: 4 residues within 4Å: Chain A: H.64, D.66, H.79, H.92 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.64, A:D.66, A:H.79, A:H.92

3 x CA: CALCIUM ION(Non-covalent)

CA.3: 6 residues within 4Å: Chain A: D.71, G.72, G.74, I.76, D.94, E.97 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.71, A:G.72, A:G.74, A:I.76, A:D.94, A:E.97 CA.4: 5 residues within 4Å: Chain A: D.54, G.86, I.87, G.88, D.90 6 PLIP interactions: 4 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.54, A:G.86, A:G.88, A:D.90, H2O.2, H2O.2 CA.5: 3 residues within 4Å: Chain A: D.20, E.95, E.97 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.20, A:E.95, A:E.95, H2O.6, H2O.6

1 x BR: BROMIDE ION(Non-covalent)

BR.6: 2 residues within 4Å: Chain A: H.68, F.81 Ligand excluded by PLIP

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 5 residues within 4Å: Chain A: L.77, G.105, T.106, Y.136 Ligands: R47.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.106 EDO.8: 3 residues within 4Å: Chain A: P.19, M.21, N.22 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.19 Water bridges: A:R.23

1 x R47: N-[(2S)-3-[(S)-(4-bromophenyl)(hydroxy)phosphoryl]-2-{[3-(3'-chlorobiphenyl-4-yl)-1,2-oxazol-5-yl]methyl}propanoyl]-L-alpha-glutamyl-L-alpha-glutamine(Non-covalent)

R47.9: 26 residues within 4Å: Chain A: G.74, G.75, I.76, L.77, A.78, H.79, L.110, T.111, H.114, E.115, H.118, H.124, P.128, K.129, A.130, V.131, F.133, P.134, T.135, Y.136, A.137, Y.138, V.139 Ligands: ZN.1, EDO.7, 6PJ.10 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.76, A:H.79, A:H.114, A:Y.136, A:A.137 Hydrogen bonds: A:G.75, A:P.134, A:Y.136 Water bridges: A:G.74, A:G.75, A:Y.136 pi-Stacking: A:H.114

1 x 6PJ: CY5.5-PEG2(Non-functional Binders)

6PJ.10: 1 residues within 4Å: Ligands: R47.9 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bordenave, T. et al., Synthesis and in Vitro and in Vivo Evaluation of MMP-12 Selective Optical Probes. Bioconjug.Chem. (2016)

Release Date

2016-09-14

Peptides

Macrophage metalloelastase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Macrophage metalloelastase

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