SMTL ID : 4i03.1

Human MMP12 in complex with a PEG-linked bifunctional L-glutamate motif inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 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: L88.6 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: 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.2 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

1 x L88: (4R,22R)-5,21-dioxo-4,22-bis({3-[4-(4-phenylthiophen-2-yl)phenyl]propanoyl}amino)-10,13,16-trioxa-6,20-diazapentacosane-1,25-dioic acid(Non-covalent)

L88.6: 20 residues within 4Å: Chain A: G.75, I.76, L.77, A.78, L.110, T.111, H.114, H.118, H.124, P.128, K.129, A.130, V.131, F.133, P.134, T.135, Y.136, K.137 Ligands: ZN.1, PGO.11 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:I.76, A:H.114, A:V.131, A:Y.136, A:K.137 Hydrogen bonds: A:L.77, A:A.78 Water bridges: A:P.134 Salt bridges: A:H.114, A:H.118, A:H.124 pi-Stacking: A:H.114

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: M.21, N.22, D.25, T.100, T.101, H.102 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.22, A:D.25, A:T.101 Water bridges: A:T.101 GOL.8: 5 residues within 4Å: Chain A: M.1, G.2, V.4, R.6, L.157 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:M.1, A:M.1, A:G.2, A:R.6, A:R.6, A:L.157 GOL.9: 6 residues within 4Å: Chain A: M.1, G.121, L.122, G.123, S.156, L.157 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.1, A:G.123, A:S.156

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

PGO.10: 1 residues within 4Å: Chain A: R.152 No protein-ligand interaction detected (PLIP) PGO.11: 4 residues within 4Å: Chain A: G.75, T.135, Y.136 Ligands: L88.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.136

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

DMS.12: 5 residues within 4Å: Chain A: H.68, H.79, A.80, F.81 Ligands: EDO.16 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.80 pi-Cation interactions: A:H.68, A:F.81 DMS.13: 3 residues within 4Å: Chain A: F.133, T.135, K.137 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.137

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

EDO.14: 5 residues within 4Å: Chain A: R.61, G.62, G.72, D.96 Ligands: EDO.15 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.61, A:D.96 EDO.15: 2 residues within 4Å: Chain A: D.71 Ligands: EDO.14 No protein-ligand interaction detected (PLIP) EDO.16: 4 residues within 4Å: Chain A: A.80, H.118, H.124 Ligands: DMS.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.80 EDO.17: 5 residues within 4Å: Chain A: L.56, H.64, G.65, D.66, H.92 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.64

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

PEG.18: 2 residues within 4Å: Chain A: T.41, P.42 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.41

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: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Macrophage metalloelastase