SMTL ID : 4p3c.1

MT1-MMP:Fab complex (Form I)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

hetero-2-2-2-mer

Ligands

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 4 residues within 4Å: Chain A: S.52, G.54, G.55, R.56 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain D: S.52, G.54, G.55, R.56 Ligand excluded by PLIP

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

EPE.2: 5 residues within 4Å: Chain A: G.55, R.56, R.72, D.73, N.74 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.56, A:R.72, A:N.74, A:N.74 EPE.14: 5 residues within 4Å: Chain D: G.55, R.56, R.72, D.73, N.74 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.56, D:R.72, D:N.74, D:N.74

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

EDO.3: 6 residues within 4Å: Chain A: A.24, S.25, N.77 Chain D: N.138, S.139, M.140 6 PLIP interactions: 3 interactions with chain D, 3 interactions with chain A Hydrogen bonds: D:S.139, D:M.140, D:M.140, A:N.77 Water bridges: A:R.76, A:N.77 EDO.4: 7 residues within 4Å: Chain A: P.131, G.132, S.133, A.134 Chain B: S.122, I.123, F.124 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:I.123, A:S.133 Water bridges: B:V.121, A:S.133 EDO.5: 6 residues within 4Å: Chain A: Q.39, T.40, P.41, K.43, M.93, L.113 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.43 EDO.6: 6 residues within 4Å: Chain A: E.153, P.154, V.155, P.172, A.173, L.182 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.155, A:V.155, A:A.173 EDO.7: 4 residues within 4Å: Chain A: Y.59 Chain B: S.97, H.98, A.99 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:A.99, C:D.2 EDO.11: 4 residues within 4Å: Chain B: H.31, N.33 Chain C: F.1, N.11 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:N.33, C:N.11, C:N.11 EDO.15: 6 residues within 4Å: Chain A: N.138, S.139, M.140 Chain D: A.24, S.25, N.77 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain D Hydrogen bonds: A:S.139, A:M.140, A:M.140, D:N.77 Water bridges: D:R.76, D:N.77 EDO.16: 7 residues within 4Å: Chain D: P.131, G.132, S.133, A.134 Chain E: S.122, I.123, F.124 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain E Hydrogen bonds: D:S.133, E:I.123 Water bridges: D:S.133, E:V.121 EDO.17: 6 residues within 4Å: Chain D: Q.39, T.40, P.41, K.43, M.93, L.113 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.43 EDO.18: 6 residues within 4Å: Chain D: E.153, P.154, V.155, P.172, A.173, L.182 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.155, D:V.155, D:A.173 EDO.19: 4 residues within 4Å: Chain D: Y.59 Chain E: S.97, H.98, A.99 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Hydrogen bonds: D:Y.59, E:A.99 EDO.23: 4 residues within 4Å: Chain E: H.31, N.33 Chain F: F.1, N.11 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain F Hydrogen bonds: E:N.33, F:N.11, F:N.11

6 x ACT: ACETATE ION(Non-functional Binders)

ACT.8: 8 residues within 4Å: Chain A: F.171, P.172, V.174, T.181, L.182, S.183 Chain B: S.168, S.182 6 PLIP interactions: 3 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:S.168, B:S.182, B:S.182, A:S.183 Hydrophobic interactions: A:V.174 Water bridges: A:S.183 ACT.9: 5 residues within 4Å: Chain A: N.100, Y.101, S.103 Chain B: Y.54, F.60 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:N.100 Hydrogen bonds: A:N.100 Water bridges: B:S.61 ACT.12: 3 residues within 4Å: Chain B: K.44, E.86, D.87 4 PLIP interactions: 4 interactions with chain B Water bridges: B:K.44, B:K.44, B:R.66 Salt bridges: B:K.44 ACT.20: 8 residues within 4Å: Chain D: F.171, P.172, V.174, T.181, L.182, S.183 Chain E: S.168, S.182 6 PLIP interactions: 3 interactions with chain E, 3 interactions with chain D Hydrogen bonds: E:S.168, E:S.182, E:S.182, D:S.183 Hydrophobic interactions: D:V.174 Water bridges: D:S.183 ACT.21: 5 residues within 4Å: Chain D: N.100, Y.101, S.103 Chain E: Y.54, F.60 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain D Water bridges: E:S.61 Hydrophobic interactions: D:N.100 Hydrogen bonds: D:N.100 ACT.24: 3 residues within 4Å: Chain E: K.44, E.86, D.87 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain E Water bridges: B:E.84, E:K.44, E:K.44, E:R.66 Salt bridges: E:K.44

2 x MG: MAGNESIUM ION(Non-covalent)

MG.10: 1 residues within 4Å: Chain B: D.17 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.17, H2O.9, H2O.9, H2O.10 MG.22: 1 residues within 4Å: Chain E: D.17 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.17, H2O.23, H2O.24, H2O.25

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Udi, Y. et al., Inhibition mechanism of membrane metalloprotease by an exosite-swiveling conformational antibody. Structure (2015)

Release Date

2014-12-17

Peptides

Heavy Chain Fab fragment of antibody LEM-2/15: AD
Light Chain Fab fragment of antibody LEM-2/15: BE
Matrix metalloproteinase-14: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
H

D
H

B
L

E
L

C
M

F
M

Heavy Chain Fab fragment of antibody LEM-2/15

Light Chain Fab fragment of antibody LEM-2/15

Matrix metalloproteinase-14

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