SMTL ID : 5l79.1

Crystal structure of MMP12 in complex with RXP470.1 conjugated with fluorophore Cy5,5 in space group P21212.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 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: R47.6 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.1, H2O.1 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.3, H2O.3

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)

R47.6: 25 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, K.137, V.139, F.144 Ligands: ZN.1, 6PJ.7 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:H.79, A:H.114, A:V.131, A:Y.136, A:K.137 Hydrogen bonds: A:G.75, A:G.75, A:P.134, A:Y.136, A:Y.136 Water bridges: A:A.80 pi-Stacking: A:H.114

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

6PJ.7: 9 residues within 4Å: Chain A: K.129, Y.136, K.137, T.143, R.145, L.146, S.147, A.148 Ligands: R47.6 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:K.129, A:Y.136, A:R.145 Hydrogen bonds: A:A.148 Water bridges: A:R.145 Salt bridges: A:K.129, A:K.129, A:R.145 pi-Cation interactions: A:K.129, A:R.145

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

EDO.8: 2 residues within 4Å: Chain A: G.84, S.85 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.85 EDO.9: 4 residues within 4Å: Chain A: P.3, G.82, P.83, G.88 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.82 EDO.10: 1 residues within 4Å: Chain A: Y.9 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.9 EDO.11: 4 residues within 4Å: Chain A: A.53, D.54, S.85, G.86 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.86 Water bridges: A:M.52, A:D.54

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 2 residues within 4Å: Chain A: V.58, H.64 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.92

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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