SMTL ID : 3kd4.3 (2 other biounits)

CRYSTAL STRUCTURE OF A PUTATIVE PROTEASE (BDI_1141) FROM PARABACTEROIDES DISTASONIS ATCC 8503 AT 2.00 A RESOLUTION

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 7 residues within 4Å: Chain A: L.237, H.254, N.258 Chain B: L.237, H.254, N.258 Ligands: PO4.13 11 PLIP interactions: 5 interactions with chain B, 6 interactions with chain A Hydrogen bonds: B:N.258, A:N.258 Water bridges: B:N.257, B:N.257, B:N.258, A:N.257, A:N.257, A:N.257, A:N.258 Salt bridges: B:H.254, A:H.254 PO4.2: 5 residues within 4Å: Chain A: E.24, R.26, H.60, S.117 Ligands: GOL.11 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.24, A:E.24, A:S.117 Water bridges: A:R.26, A:R.26, A:H.60 Salt bridges: A:R.26, A:H.60 PO4.3: 4 residues within 4Å: Chain A: E.151, G.152, T.153, K.175 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.152 Water bridges: A:T.153, A:K.175 Salt bridges: A:K.175 PO4.13: 7 residues within 4Å: Chain A: L.237, H.254, N.258 Chain B: L.237, H.254, N.258 Ligands: PO4.1 11 PLIP interactions: 6 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:N.258, A:N.258 Water bridges: B:N.257, B:N.257, B:N.257, B:N.258, A:N.257, A:N.257, A:N.258 Salt bridges: B:H.254, A:H.254 PO4.14: 5 residues within 4Å: Chain B: E.24, R.26, H.60, S.117 Ligands: GOL.23 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:E.24, B:E.24, B:S.117 Water bridges: B:R.26, B:R.26, B:H.60 Salt bridges: B:R.26, B:H.60 PO4.15: 4 residues within 4Å: Chain B: E.151, G.152, T.153, K.175 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.152 Water bridges: B:T.153, B:K.175 Salt bridges: B:K.175

18 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: Q.23, Y.125, A.127, L.128, D.129, Y.271 Ligand excluded by PLIP GOL.5: 4 residues within 4Å: Chain A: P.84, R.85, F.86, E.98 Ligand excluded by PLIP GOL.6: 5 residues within 4Å: Chain A: Y.8, K.13, S.27, M.29, E.136 Ligand excluded by PLIP GOL.7: 3 residues within 4Å: Chain A: H.36, E.107, L.108 Ligand excluded by PLIP GOL.8: 5 residues within 4Å: Chain A: A.156, P.209, S.210, D.318, A.319 Ligand excluded by PLIP GOL.9: 5 residues within 4Å: Chain A: F.192, Q.193, R.349, E.418, L.419 Ligand excluded by PLIP GOL.10: 7 residues within 4Å: Chain A: P.287, A.291, L.328, A.329, V.330, L.341, S.342 Ligand excluded by PLIP GOL.11: 4 residues within 4Å: Chain A: T.16, H.18, E.24 Ligands: PO4.2 Ligand excluded by PLIP GOL.12: 2 residues within 4Å: Chain A: H.171, D.172 Ligand excluded by PLIP GOL.16: 6 residues within 4Å: Chain B: Q.23, Y.125, A.127, L.128, D.129, Y.271 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain B: P.84, R.85, F.86, E.98 Ligand excluded by PLIP GOL.18: 5 residues within 4Å: Chain B: Y.8, K.13, S.27, M.29, E.136 Ligand excluded by PLIP GOL.19: 3 residues within 4Å: Chain B: H.36, E.107, L.108 Ligand excluded by PLIP GOL.20: 5 residues within 4Å: Chain B: A.156, P.209, S.210, D.318, A.319 Ligand excluded by PLIP GOL.21: 5 residues within 4Å: Chain B: F.192, Q.193, R.349, E.418, L.419 Ligand excluded by PLIP GOL.22: 7 residues within 4Å: Chain B: P.287, A.291, L.328, A.329, V.330, L.341, S.342 Ligand excluded by PLIP GOL.23: 4 residues within 4Å: Chain B: T.16, H.18, E.24 Ligands: PO4.14 Ligand excluded by PLIP GOL.24: 2 residues within 4Å: Chain B: H.171, D.172 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of Putative proteases (YP_001302526.1) from Parabacteroides distasonis ATCC 8503 at 2.00 A resolution. To be published

Release Date

2009-11-24

Peptides

Putative protease: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

Putative protease

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