SMTL ID : 4h30.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.43 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: 0ZD.17 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.12: 4 residues within 4Å: Chain B: H.114, H.118, H.124 Ligands: 0ZD.17 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.114, B:H.118, B:H.124 ZN.13: 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.1, H2O.1 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.14: 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.11 CA.15: 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:D.20, B:E.95, B:E.97, H2O.10 CA.16: 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

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 5 residues within 4Å: Chain A: N.39, V.40, T.41, P.42, Q.155 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.155 Water bridges: A:G.159 GOL.7: 5 residues within 4Å: Chain A: G.65, D.66, H.68, F.81, I.87 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.68 GOL.8: 4 residues within 4Å: Chain A: Y.28, K.32, F.109, I.141 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.32 GOL.9: 6 residues within 4Å: Chain A: V.4, W.5, R.6, P.83, G.84, S.85 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.4, A:R.6, A:S.85 Water bridges: A:R.6, A:K.7 GOL.10: 6 residues within 4Å: Chain A: P.128, K.129, A.130, V.131, K.137, V.139 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Water bridges: B:D.71, A:P.128, A:V.131, A:K.137 Hydrogen bonds: A:A.130 GOL.11: 4 residues within 4Å: Chain A: H.68, H.79, A.80, F.81 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.80 Water bridges: A:H.79, A:G.82 GOL.18: 7 residues within 4Å: Chain B: M.1, G.121, L.122, G.123, G.153, S.156, L.157 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:M.1, B:G.123, B:G.123, B:S.156, B:S.156 GOL.19: 4 residues within 4Å: Chain B: S.125, S.126, P.134 Ligands: 0ZD.17 No protein-ligand interaction detected (PLIP)

1 x 0ZD: N,N'-bis(2-[(biphenyl-4ylsulfonyl)[(2R)-1-hydroxy-3-methyl-1-oxobutan-2-yl]-amino]ethyl)benzene-1,3-dicarboxamide(Non-covalent)

0ZD.17: 32 residues within 4Å: Chain A: I.76, L.77, A.78, 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, 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.12, GOL.19, PEG.20 28 PLIP interactions: 12 interactions with chain A, 16 interactions with chain B Hydrophobic interactions: A:I.76, A:H.114, A:P.134, A:Y.136, B:I.76, B:L.77, B:H.114, B:P.134, B:P.134, B:Y.136, B:Y.136 Hydrogen bonds: A:L.77, A:A.78, A:A.78, B:A.78, B:T.135, B:T.135 Water bridges: A:P.134, B:H.124, B:P.134 Salt bridges: A:H.114, A:H.118, A:H.124, B:H.114, B:H.118, B:H.124 pi-Stacking: A:H.114, B:H.114

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

PEG.20: 5 residues within 4Å: Chain A: P.128 Chain B: D.67, H.68, H.79 Ligands: 0ZD.17 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.68, B:H.79 Water bridges: B:A.80

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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