SMTL ID : 3g0k.1

Crystal structure of a protein of unknown function with a cystatin-like fold (saro_2880) from novosphingobium aromaticivorans dsm at 1.30 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-dimer

Ligands

2 x CA: CALCIUM ION(Non-covalent)

CA.1: 5 residues within 4Å: Chain A: A.21, E.26 Chain B: A.21, E.26 Ligands: CA.8 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:A.21, B:E.26, A:A.21, H2O.3, H2O.10 CA.8: 5 residues within 4Å: Chain A: A.21, E.26 Chain B: A.21, E.26 Ligands: CA.1 5 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:A.21, A:E.26, B:A.21, H2O.3, H2O.10

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

ACT.2: 6 residues within 4Å: Chain A: D.84, A.85, R.86, E.106, W.108, P.109 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.106 Water bridges: A:W.108 Salt bridges: A:R.86 ACT.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) ACT.9: 6 residues within 4Å: Chain B: D.84, A.85, R.86, E.106, W.108, P.109 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:E.106 Water bridges: B:W.108 Salt bridges: B:R.86 ACT.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

8 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.4: 8 residues within 4Å: Chain A: Y.37, L.41, Q.59, A.64, L.71, D.118, F.120, H.130 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.37, A:L.41, A:L.71, A:F.120 Hydrogen bonds: A:Q.59, A:Q.59 Water bridges: A:D.132 MPD.5: 9 residues within 4Å: Chain A: L.41, F.74, L.75, V.78, P.83, A.85, Q.87, V.105 Ligands: MPD.7 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.74, A:L.75, A:V.78, A:P.83, A:A.85, A:Q.87, A:V.105 MPD.6: 5 residues within 4Å: Chain A: L.63, R.107, I.134, D.136 Chain B: Q.135 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.63 Hydrogen bonds: A:R.107, A:D.136 Water bridges: A:I.134, A:I.134, A:D.136 MPD.7: 3 residues within 4Å: Chain A: A.64, L.114 Ligands: MPD.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.64 MPD.11: 8 residues within 4Å: Chain B: Y.37, L.41, Q.59, A.64, L.71, D.118, F.120, H.130 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.37, B:L.41, B:L.71, B:F.120 Hydrogen bonds: B:Q.59, B:Q.59 MPD.12: 9 residues within 4Å: Chain B: L.41, F.74, L.75, V.78, P.83, A.85, Q.87, V.105 Ligands: MPD.14 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.74, B:L.75, B:V.78, B:P.83, B:A.85, B:Q.87, B:V.105 MPD.13: 5 residues within 4Å: Chain A: Q.135 Chain B: L.63, R.107, I.134, D.136 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:L.63 Hydrogen bonds: B:R.107, B:D.136 Water bridges: B:I.134, B:I.134, B:D.136, B:D.136 MPD.14: 3 residues within 4Å: Chain B: A.64, L.114 Ligands: MPD.12 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:A.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of protein of unknown function with a cystatin-like fold (YP_498150.1) from Novosphingobium aromaticivorans DSM 12444 at 1.30 A resolution. To be published

Release Date

2009-02-10

Peptides

Putative membrane protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Putative membrane protein