SMTL ID : 4h49.1 (1 other biounit)

Crystal structure of the catalytic domain of MMP-12 in complex with a twin inhibitor.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.114, H.118, H.124 Ligands: L29.10 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 ZN.11: 4 residues within 4Å: Chain B: H.114, H.118, H.124 Ligands: L29.10 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.114, B:H.118, B:H.124 ZN.12: 4 residues within 4Å: Chain B: H.64, D.66, H.79, H.92 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.64, B:D.66, B:H.79, B:H.92

6 x CA: CALCIUM ION(Non-covalent)

CA.3: 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.4: 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.1, H2O.1 CA.5: 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.13: 5 residues within 4Å: Chain B: D.54, G.86, I.87, G.88, D.90 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.54, B:G.86, B:G.88, B:D.90, H2O.4 CA.14: 3 residues within 4Å: Chain B: D.20, E.95, E.97 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.20, B:E.95, B:E.95, B:E.97, H2O.3 CA.15: 6 residues within 4Å: Chain B: D.71, G.72, G.74, I.76, D.94, E.97 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:D.71, B:G.72, B:G.74, B:I.76, B:D.94, B:E.97

2 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.6: 4 residues within 4Å: Chain A: R.61, G.62, A.63 Ligands: DMS.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.63, A:A.63 PGO.9: 5 residues within 4Å: Chain A: I.14, N.15, Y.17, R.23 Ligands: PEG.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.23, A:R.23

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.7: 3 residues within 4Å: Chain A: R.61, H.64 Ligands: PGO.6 No protein-ligand interaction detected (PLIP)

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 4 residues within 4Å: Chain A: N.16, Y.17, R.23 Ligands: PGO.9 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.17 Water bridges: A:R.23 PEG.16: 6 residues within 4Å: Chain A: K.73, G.74, G.75 Chain B: Y.136, K.137, Y.138 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.138 Water bridges: B:Y.136

1 x L29: N,N'-bis(2-{(biphenyl-4-ylsulfonyl)[(2R)-1-(hydroxyamino)-3-methyl-1-oxobutan-2-yl]amino}ethyl)benzene-1,3-dicarboxamide (non-preferred name)(Non-covalent)

L29.10: 33 residues within 4Å: Chain A: I.76, L.77, A.78, H.79, L.110, T.111, H.114, E.115, H.118, H.124, V.131, F.133, P.134, T.135, Y.136 Chain B: I.76, L.77, A.78, H.79, L.110, T.111, H.114, E.115, H.118, H.124, V.131, F.133, P.134, T.135, Y.136 Ligands: ZN.1, ZN.11, GOL.17 20 PLIP interactions: 11 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:L.110, B:H.114, B:V.131, B:P.134, B:Y.136, A:I.76, A:L.110, A:H.114, A:P.134, A:Y.136 Hydrogen bonds: B:L.77, B:A.78, B:A.78, B:P.134, A:L.77, A:A.78, A:A.78 Water bridges: B:P.134, A:P.134 pi-Stacking: B:H.114

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.17: 9 residues within 4Å: Chain B: K.129, A.130, V.131, T.135, Y.136, K.137, V.139, F.144 Ligands: L29.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.129, B:T.135, B:K.137 Water bridges: B:V.131

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Antoni, C. et al., Crystallization of bi-functional ligand protein complexes. J.Struct.Biol. (2013)

Release Date

2013-04-24

Peptides

Macrophage metalloelastase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Macrophage metalloelastase

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