SMTL ID : 3m1u.1

Crystal structure of a Putative gamma-D-glutamyl-L-diamino acid endopeptidase (DVU_0896) from DESULFOVIBRIO VULGARIS HILDENBOROUGH at 1.75 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

11 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 7 residues within 4Å: Chain A: Q.152, R.153, W.294, G.295, D.302, N.321 Ligands: ACT.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.152, A:D.302, A:S.304, A:R.320, A:N.321 GOL.2: 7 residues within 4Å: Chain A: T.154, A.155, W.157, S.305, R.308, D.309, R.320 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:A.155, A:W.157, A:R.308 Water bridges: A:S.305, A:S.305, A:S.305, A:S.305, A:R.308, A:D.309 GOL.3: 8 residues within 4Å: Chain A: D.212, D.213, H.228, Q.290, E.299, D.300, R.301 Chain B: R.133 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:R.133, B:R.133, A:Q.290 Water bridges: B:R.98, B:R.133, A:D.213, A:D.213 GOL.4: 9 residues within 4Å: Chain A: G.361, H.362, M.380, W.381, G.382, L.419, R.422 Ligands: MES.7, CL.11 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:W.381, A:G.382, A:R.422 Water bridges: A:Y.292, A:H.362, A:R.384 GOL.5: 6 residues within 4Å: Chain A: E.15, G.16, R.393, Y.394, V.395 Chain B: L.92 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:E.15, A:G.16, A:Y.394, A:V.395, B:L.91 GOL.12: 7 residues within 4Å: Chain B: Q.152, R.153, W.294, G.295, D.302, N.321 Ligands: ACT.18 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.152, B:G.295, B:D.302, B:R.320 GOL.13: 7 residues within 4Å: Chain B: T.154, A.155, W.157, S.305, R.308, D.309, R.320 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:T.154, B:W.157, B:R.308 Water bridges: B:S.305, B:S.305, B:S.305, B:S.305, B:R.308 GOL.14: 8 residues within 4Å: Chain A: R.133 Chain B: D.212, D.213, H.228, Q.290, E.299, D.300, R.301 9 PLIP interactions: 5 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:H.228, B:Q.290, B:D.300, A:R.133, A:R.133 Water bridges: B:D.213, B:D.213, A:R.98, A:R.133 GOL.15: 6 residues within 4Å: Chain A: L.92 Chain B: E.15, G.16, R.393, Y.394, V.395 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.15, B:G.16, B:V.395 GOL.16: 9 residues within 4Å: Chain B: G.361, H.362, M.380, W.381, G.382, R.384, L.419, R.422 Ligands: MES.19 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:Y.292, B:Y.292, B:H.362, B:W.381, B:G.382, B:G.382, B:R.422, B:R.422 GOL.17: 5 residues within 4Å: Chain B: Q.26, D.27, R.29, N.285, M.288 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.27, B:R.29, B:N.285

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

ACT.6: 7 residues within 4Å: Chain A: D.302, C.303, S.304, N.321, S.322, G.361 Ligands: GOL.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.304, A:S.322, A:S.322, A:G.361 ACT.18: 7 residues within 4Å: Chain B: D.302, C.303, S.304, N.321, S.322, G.361 Ligands: GOL.12 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.304, B:S.322, B:S.322, B:G.361

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.7: 7 residues within 4Å: Chain A: G.143, F.148, M.150, W.294, W.381, R.393 Ligands: GOL.4 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.384, A:R.384 Salt bridges: A:R.393 MES.19: 8 residues within 4Å: Chain B: G.143, F.148, M.150, W.294, W.381, R.384, R.393 Ligands: GOL.16 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.384, B:R.393

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

CL.8: 4 residues within 4Å: Chain A: G.36, A.37, D.38, R.39 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain A: R.57, A.179, F.180, W.317, P.319 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: G.143, W.381, R.393 Ligand excluded by PLIP CL.11: 6 residues within 4Å: Chain A: G.382, I.383, R.384, L.419, R.422 Ligands: GOL.4 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain B: A.179, F.180, W.317, P.319 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain B: K.34, H.370, E.371 Ligand excluded by PLIP CL.22: 6 residues within 4Å: Chain B: R.405, P.406, G.407, N.413, G.418, L.419 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain B: G.143, W.381, R.393 Ligand excluded by PLIP CL.24: 4 residues within 4Å: Chain B: G.36, A.37, D.38, R.39 Ligand excluded by PLIP

Links

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Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of a Putative gamma-D-glutamyl-L-diamino acid endopeptidase (DVU_0896) from DESULFOVIBRIO VULGARIS HILDENBOROUGH at 1.75 A resolution. To be Published

Release Date

2010-04-07

Peptides

Putative gamma-D-glutamyl-L-diamino acid endopeptidase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Putative gamma-D-glutamyl-L-diamino acid endopeptidase