SMTL ID : 3ljz.4 (3 other biounits)

Crystal Structure of Human MMP-13 complexed with an Amino-2-indanol compound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 7 residues within 4Å: Chain A: A.58, D.59, M.61, N.91, Y.92, G.93, D.95 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:N.91, A:D.95, H2O.1 CA.2: 6 residues within 4Å: Chain A: D.76, G.77, S.79, L.81, D.99, E.102 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.76, A:G.77, A:S.79, A:L.81, A:D.99, A:E.102

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: H.69, D.71, H.84, H.97 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.69, A:D.71, A:H.84, A:H.97 ZN.4: 4 residues within 4Å: Chain A: H.119, H.123, H.129 Ligands: LA3.10 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.119, A:H.123, A:H.129

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.5: 6 residues within 4Å: Chain A: Y.73, L.81, H.84, A.85, F.86, P.87 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:H.84 EPE.6: 8 residues within 4Å: Chain A: M.26, E.30, K.33, A.34, K.37, S.106, N.112, F.114 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.34, A:K.37 Water bridges: A:F.114

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 3 residues within 4Å: Chain A: E.32, K.36, R.52 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:E.32 Water bridges: A:Y.17, A:R.52, A:R.52 Salt bridges: A:K.36, A:R.52 SO4.8: 3 residues within 4Å: Chain A: K.12, M.13, N.14 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:M.13, A:N.14, A:N.14 SO4.9: 2 residues within 4Å: Chain A: P.5, R.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.6 Salt bridges: A:R.6

1 x LA3: (2R)-2-[4-(1,3-benzodioxol-5-yl)benzyl]-N~4~-hydroxy-N~1~-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]butanediamide(Non-covalent)

LA3.10: 19 residues within 4Å: Chain A: G.80, L.81, L.82, A.83, H.84, L.115, H.119, E.120, H.123, H.129, A.135, L.136, F.138, P.139, I.140, Y.141, T.142, T.144 Ligands: ZN.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.81, A:H.119, A:L.136, A:Y.141 Hydrogen bonds: A:L.82, A:A.83, A:P.139, A:P.139, A:Y.141 pi-Stacking: A:H.119

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shieh, H.S. et al., Structure analysis reveals the flexibility of the ADAMTS-5 active site. Protein Sci. (2011)

Release Date

2011-02-02

Peptides

Collagenase 3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Collagenase 3

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