SMTL ID : 1su3.3 (2 other biounits)

X-ray structure of human proMMP-1: New insights into collagenase action

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-octamer

Ligands

32 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: A.138, D.139, G.171, G.173, D.175 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.139, A:G.171, A:G.173, A:D.175 CA.2: 6 residues within 4Å: Chain A: D.156, G.157, G.159, N.161, D.179, E.182 6 PLIP interactions: 6 interactions with chain A Metal complexes: A:D.156, A:G.157, A:G.159, A:N.161, A:D.179, A:E.182 CA.3: 4 residues within 4Å: Chain A: T.103, D.105, E.180, E.182 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.105, A:E.180, A:E.180, A:E.182, H2O.7 CA.4: 4 residues within 4Å: Chain A: D.266, E.310, D.359, D.408 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.266, A:E.310, A:D.359, H2O.6, H2O.6 CA.14: 5 residues within 4Å: Chain B: A.138, D.139, G.171, G.173, D.175 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.139, B:G.171, B:G.173, B:D.175 CA.15: 6 residues within 4Å: Chain B: D.156, G.157, G.159, N.161, D.179, E.182 6 PLIP interactions: 6 interactions with chain B Metal complexes: B:D.156, B:G.157, B:G.159, B:N.161, B:D.179, B:E.182 CA.16: 4 residues within 4Å: Chain B: T.103, D.105, E.180, E.182 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.105, B:E.180, B:E.180, B:E.182, H2O.14 CA.17: 4 residues within 4Å: Chain B: D.266, E.310, D.359, D.408 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.266, B:E.310, B:D.359, H2O.13, H2O.13 CA.27: 5 residues within 4Å: Chain C: A.138, D.139, G.171, G.173, D.175 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:D.139, C:G.171, C:G.173, C:D.175 CA.28: 6 residues within 4Å: Chain C: D.156, G.157, G.159, N.161, D.179, E.182 6 PLIP interactions: 6 interactions with chain C Metal complexes: C:D.156, C:G.157, C:G.159, C:N.161, C:D.179, C:E.182 CA.29: 4 residues within 4Å: Chain C: T.103, D.105, E.180, E.182 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.105, C:E.180, C:E.180, C:E.182, H2O.21 CA.30: 4 residues within 4Å: Chain C: D.266, E.310, D.359, D.408 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.266, C:E.310, C:D.359, H2O.20, H2O.20 CA.40: 5 residues within 4Å: Chain D: A.138, D.139, G.171, G.173, D.175 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:D.139, D:G.171, D:G.173, D:D.175 CA.41: 6 residues within 4Å: Chain D: D.156, G.157, G.159, N.161, D.179, E.182 6 PLIP interactions: 6 interactions with chain D Metal complexes: D:D.156, D:G.157, D:G.159, D:N.161, D:D.179, D:E.182 CA.42: 4 residues within 4Å: Chain D: T.103, D.105, E.180, E.182 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.105, D:E.180, D:E.180, D:E.182, H2O.28 CA.43: 4 residues within 4Å: Chain D: D.266, E.310, D.359, D.408 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.266, D:E.310, D:D.359, H2O.26, H2O.26 CA.53: 5 residues within 4Å: Chain E: A.138, D.139, G.171, G.173, D.175 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:D.139, E:G.171, E:G.173, E:D.175 CA.54: 6 residues within 4Å: Chain E: D.156, G.157, G.159, N.161, D.179, E.182 6 PLIP interactions: 6 interactions with chain E Metal complexes: E:D.156, E:G.157, E:G.159, E:N.161, E:D.179, E:E.182 CA.55: 4 residues within 4Å: Chain E: T.103, D.105, E.180, E.182 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.105, E:E.180, E:E.180, E:E.182, H2O.35 CA.56: 4 residues within 4Å: Chain E: D.266, E.310, D.359, D.408 5 PLIP interactions: 3 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.266, E:E.310, E:D.359, H2O.33, H2O.33 CA.66: 5 residues within 4Å: Chain F: A.138, D.139, G.171, G.173, D.175 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:D.139, F:G.171, F:G.173, F:D.175 CA.67: 6 residues within 4Å: Chain F: D.156, G.157, G.159, N.161, D.179, E.182 6 PLIP interactions: 6 interactions with chain F Metal complexes: F:D.156, F:G.157, F:G.159, F:N.161, F:D.179, F:E.182 CA.68: 4 residues within 4Å: Chain F: T.103, D.105, E.180, E.182 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.105, F:E.180, F:E.180, F:E.182, H2O.41 CA.69: 4 residues within 4Å: Chain F: D.266, E.310, D.359, D.408 5 PLIP interactions: 3 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.266, F:E.310, F:D.359, H2O.40, H2O.40 CA.79: 5 residues within 4Å: Chain G: A.138, D.139, G.171, G.173, D.175 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:D.139, G:G.171, G:G.173, G:D.175 CA.80: 6 residues within 4Å: Chain G: D.156, G.157, G.159, N.161, D.179, E.182 6 PLIP interactions: 6 interactions with chain G Metal complexes: G:D.156, G:G.157, G:G.159, G:N.161, G:D.179, G:E.182 CA.81: 4 residues within 4Å: Chain G: T.103, D.105, E.180, E.182 5 PLIP interactions: 4 interactions with chain G, 1 Ligand-Water interactions Metal complexes: G:D.105, G:E.180, G:E.180, G:E.182, H2O.48 CA.82: 4 residues within 4Å: Chain G: D.266, E.310, D.359, D.408 5 PLIP interactions: 3 interactions with chain G, 2 Ligand-Water interactions Metal complexes: G:D.266, G:E.310, G:D.359, H2O.47, H2O.47 CA.92: 5 residues within 4Å: Chain H: A.138, D.139, G.171, G.173, D.175 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:D.139, H:G.171, H:G.173, H:D.175 CA.93: 6 residues within 4Å: Chain H: D.156, G.157, G.159, N.161, D.179, E.182 6 PLIP interactions: 6 interactions with chain H Metal complexes: H:D.156, H:G.157, H:G.159, H:N.161, H:D.179, H:E.182 CA.94: 4 residues within 4Å: Chain H: T.103, D.105, E.180, E.182 5 PLIP interactions: 4 interactions with chain H, 1 Ligand-Water interactions Metal complexes: H:D.105, H:E.180, H:E.180, H:E.182, H2O.55 CA.95: 4 residues within 4Å: Chain H: D.266, E.310, D.359, D.408 5 PLIP interactions: 3 interactions with chain H, 2 Ligand-Water interactions Metal complexes: H:D.266, H:E.310, H:D.359, H2O.54, H2O.54

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

CL.5: 9 residues within 4Å: Chain A: A.267, I.268, A.311, A.312, A.360, A.361, A.409, V.410 Ligands: NA.6 Ligand excluded by PLIP CL.18: 9 residues within 4Å: Chain B: A.267, I.268, A.311, A.312, A.360, A.361, A.409, V.410 Ligands: NA.19 Ligand excluded by PLIP CL.31: 9 residues within 4Å: Chain C: A.267, I.268, A.311, A.312, A.360, A.361, A.409, V.410 Ligands: NA.32 Ligand excluded by PLIP CL.44: 9 residues within 4Å: Chain D: A.267, I.268, A.311, A.312, A.360, A.361, A.409, V.410 Ligands: NA.45 Ligand excluded by PLIP CL.57: 9 residues within 4Å: Chain E: A.267, I.268, A.311, A.312, A.360, A.361, A.409, V.410 Ligands: NA.58 Ligand excluded by PLIP CL.70: 9 residues within 4Å: Chain F: A.267, I.268, A.311, A.312, A.360, A.361, A.409, V.410 Ligands: NA.71 Ligand excluded by PLIP CL.83: 9 residues within 4Å: Chain G: A.267, I.268, A.311, A.312, A.360, A.361, A.409, V.410 Ligands: NA.84 Ligand excluded by PLIP CL.96: 9 residues within 4Å: Chain H: A.267, I.268, A.311, A.312, A.360, A.361, A.409, V.410 Ligands: NA.97 Ligand excluded by PLIP

8 x NA: SODIUM ION(Non-functional Binders)

NA.6: 5 residues within 4Å: Chain A: I.268, A.312, A.361, V.410 Ligands: CL.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.410 NA.19: 5 residues within 4Å: Chain B: I.268, A.312, A.361, V.410 Ligands: CL.18 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.312 NA.32: 5 residues within 4Å: Chain C: I.268, A.312, A.361, V.410 Ligands: CL.31 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:I.268 NA.45: 5 residues within 4Å: Chain D: I.268, A.312, A.361, V.410 Ligands: CL.44 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:A.361 NA.58: 5 residues within 4Å: Chain E: I.268, A.312, A.361, V.410 Ligands: CL.57 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:A.361 Water bridges: E:T.269 NA.71: 5 residues within 4Å: Chain F: I.268, A.312, A.361, V.410 Ligands: CL.70 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:I.268 Water bridges: F:T.269 NA.84: 5 residues within 4Å: Chain G: I.268, A.312, A.361, V.410 Ligands: CL.83 2 PLIP interactions: 2 interactions with chain G Hydrogen bonds: G:A.361 Water bridges: G:T.269 NA.97: 5 residues within 4Å: Chain H: I.268, A.312, A.361, V.410 Ligands: CL.96 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:V.410 Water bridges: H:T.269

16 x ZN: ZINC ION(Non-covalent)

ZN.7: 5 residues within 4Å: Chain A: C.73, V.75, H.199, H.203, H.209 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.73, A:H.199, A:H.203, A:H.209 ZN.8: 5 residues within 4Å: Chain A: H.149, D.151, S.153, H.164, H.177 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.149, A:D.151, A:H.164, A:H.177 ZN.20: 5 residues within 4Å: Chain B: C.73, V.75, H.199, H.203, H.209 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.73, B:H.199, B:H.203, B:H.209 ZN.21: 5 residues within 4Å: Chain B: H.149, D.151, S.153, H.164, H.177 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.149, B:D.151, B:H.164, B:H.177 ZN.33: 5 residues within 4Å: Chain C: C.73, V.75, H.199, H.203, H.209 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.73, C:H.199, C:H.203, C:H.209 ZN.34: 5 residues within 4Å: Chain C: H.149, D.151, S.153, H.164, H.177 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:H.149, C:D.151, C:H.164, C:H.177 ZN.46: 5 residues within 4Å: Chain D: C.73, V.75, H.199, H.203, H.209 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.73, D:H.199, D:H.203, D:H.209 ZN.47: 5 residues within 4Å: Chain D: H.149, D.151, S.153, H.164, H.177 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:H.149, D:D.151, D:H.164, D:H.177 ZN.59: 5 residues within 4Å: Chain E: C.73, V.75, H.199, H.203, H.209 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.73, E:H.199, E:H.203, E:H.209 ZN.60: 5 residues within 4Å: Chain E: H.149, D.151, S.153, H.164, H.177 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:H.149, E:D.151, E:H.164, E:H.177 ZN.72: 5 residues within 4Å: Chain F: C.73, V.75, H.199, H.203, H.209 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.73, F:H.199, F:H.203, F:H.209 ZN.73: 5 residues within 4Å: Chain F: H.149, D.151, S.153, H.164, H.177 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:H.149, F:D.151, F:H.164, F:H.177 ZN.85: 5 residues within 4Å: Chain G: C.73, V.75, H.199, H.203, H.209 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:C.73, G:H.199, G:H.203, G:H.209 ZN.86: 5 residues within 4Å: Chain G: H.149, D.151, S.153, H.164, H.177 4 PLIP interactions: 4 interactions with chain G Metal complexes: G:H.149, G:D.151, G:H.164, G:H.177 ZN.98: 5 residues within 4Å: Chain H: C.73, V.75, H.199, H.203, H.209 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:C.73, H:H.199, H:H.203, H:H.209 ZN.99: 5 residues within 4Å: Chain H: H.149, D.151, S.153, H.164, H.177 4 PLIP interactions: 4 interactions with chain H Metal complexes: H:H.149, H:D.151, H:H.164, H:H.177

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

SO4.9: 3 residues within 4Å: Chain A: P.170, G.171 Chain C: K.385 Ligand excluded by PLIP SO4.10: 6 residues within 4Å: Chain A: D.148, H.149, R.150, D.151, N.152, P.154 Ligand excluded by PLIP SO4.11: 3 residues within 4Å: Chain A: P.107, R.108, A.109 Ligand excluded by PLIP SO4.12: 5 residues within 4Å: Chain A: S.123, T.126, S.244, Q.245, N.246 Ligand excluded by PLIP SO4.22: 3 residues within 4Å: Chain B: P.170, G.171 Chain D: K.385 Ligand excluded by PLIP SO4.23: 6 residues within 4Å: Chain B: D.148, H.149, R.150, D.151, N.152, P.154 Ligand excluded by PLIP SO4.24: 3 residues within 4Å: Chain B: P.107, R.108, A.109 Ligand excluded by PLIP SO4.25: 5 residues within 4Å: Chain B: S.123, T.126, S.244, Q.245, N.246 Ligand excluded by PLIP SO4.35: 3 residues within 4Å: Chain B: K.385 Chain C: P.170, G.171 Ligand excluded by PLIP SO4.36: 6 residues within 4Å: Chain C: D.148, H.149, R.150, D.151, N.152, P.154 Ligand excluded by PLIP SO4.37: 3 residues within 4Å: Chain C: P.107, R.108, A.109 Ligand excluded by PLIP SO4.38: 5 residues within 4Å: Chain C: S.123, T.126, S.244, Q.245, N.246 Ligand excluded by PLIP SO4.48: 3 residues within 4Å: Chain A: K.385 Chain D: P.170, G.171 Ligand excluded by PLIP SO4.49: 6 residues within 4Å: Chain D: D.148, H.149, R.150, D.151, N.152, P.154 Ligand excluded by PLIP SO4.50: 3 residues within 4Å: Chain D: P.107, R.108, A.109 Ligand excluded by PLIP SO4.51: 5 residues within 4Å: Chain D: S.123, T.126, S.244, Q.245, N.246 Ligand excluded by PLIP SO4.61: 3 residues within 4Å: Chain E: P.170, G.171 Chain G: K.385 Ligand excluded by PLIP SO4.62: 6 residues within 4Å: Chain E: D.148, H.149, R.150, D.151, N.152, P.154 Ligand excluded by PLIP SO4.63: 3 residues within 4Å: Chain E: P.107, R.108, A.109 Ligand excluded by PLIP SO4.64: 5 residues within 4Å: Chain E: S.123, T.126, S.244, Q.245, N.246 Ligand excluded by PLIP SO4.74: 3 residues within 4Å: Chain F: P.170, G.171 Chain H: K.385 Ligand excluded by PLIP SO4.75: 6 residues within 4Å: Chain F: D.148, H.149, R.150, D.151, N.152, P.154 Ligand excluded by PLIP SO4.76: 3 residues within 4Å: Chain F: P.107, R.108, A.109 Ligand excluded by PLIP SO4.77: 5 residues within 4Å: Chain F: S.123, T.126, S.244, Q.245, N.246 Ligand excluded by PLIP SO4.87: 3 residues within 4Å: Chain F: K.385 Chain G: P.170, G.171 Ligand excluded by PLIP SO4.88: 6 residues within 4Å: Chain G: D.148, H.149, R.150, D.151, N.152, P.154 Ligand excluded by PLIP SO4.89: 3 residues within 4Å: Chain G: P.107, R.108, A.109 Ligand excluded by PLIP SO4.90: 5 residues within 4Å: Chain G: S.123, T.126, S.244, Q.245, N.246 Ligand excluded by PLIP SO4.100: 3 residues within 4Å: Chain E: K.385 Chain H: P.170, G.171 Ligand excluded by PLIP SO4.101: 6 residues within 4Å: Chain H: D.148, H.149, R.150, D.151, N.152, P.154 Ligand excluded by PLIP SO4.102: 3 residues within 4Å: Chain H: P.107, R.108, A.109 Ligand excluded by PLIP SO4.103: 5 residues within 4Å: Chain H: S.123, T.126, S.244, Q.245, N.246 Ligand excluded by PLIP

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

EPE.13: 7 residues within 4Å: Chain A: V.75, P.76, S.153, H.164, A.165, F.166, Q.167 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.153, A:H.164 Water bridges: A:Q.167 EPE.26: 7 residues within 4Å: Chain B: V.75, P.76, S.153, H.164, A.165, F.166, Q.167 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.153, B:H.164 Water bridges: B:Q.167 EPE.39: 7 residues within 4Å: Chain C: V.75, P.76, S.153, H.164, A.165, F.166, Q.167 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.153, C:H.164 Water bridges: C:Q.167 EPE.52: 7 residues within 4Å: Chain D: V.75, P.76, S.153, H.164, A.165, F.166, Q.167 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:S.153, D:H.164 Water bridges: D:Q.167 EPE.65: 7 residues within 4Å: Chain E: V.75, P.76, S.153, H.164, A.165, F.166, Q.167 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.153, E:H.164 Water bridges: E:Q.167 EPE.78: 7 residues within 4Å: Chain F: V.75, P.76, S.153, H.164, A.165, F.166, Q.167 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:S.153, F:H.164 Water bridges: F:Q.167 EPE.91: 7 residues within 4Å: Chain G: V.75, P.76, S.153, H.164, A.165, F.166, Q.167 3 PLIP interactions: 3 interactions with chain G Hydrogen bonds: G:S.153, G:H.164 Water bridges: G:Q.167 EPE.104: 7 residues within 4Å: Chain H: V.75, P.76, S.153, H.164, A.165, F.166, Q.167 3 PLIP interactions: 3 interactions with chain H Hydrogen bonds: H:S.153, H:H.164 Water bridges: H:Q.167

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jozic, D. et al., X-ray structure of human proMMP-1: new insights into procollagenase activation and collagen binding. J.Biol.Chem. (2005)

Release Date

2004-12-21

Peptides

Interstitial collagenase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

C
B

D
B

E
B

F
B

G
B

H
B

Interstitial collagenase

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