SMTL ID : 3fka.1

CRYSTAL STRUCTURE OF A NTF-2 LIKE PROTEIN OF UNKNOWN FUNCTION (SPO1084) FROM SILICIBACTER POMEROYI DSS-3 AT 1.69 A RESOLUTION

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.69 Å

Oligo State

homo-tetramer

Ligands

9 x UNL: UNKNOWN LIGAND

UNL.1: 10 residues within 4Å: Chain A: Y.18, M.22, E.40, N.90, W.92, F.97, D.99, K.115, Y.117 Ligands: UNL.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.18, A:N.90, A:K.115 UNL.2: 8 residues within 4Å: Chain A: M.22, E.40, F.56, M.59, C.60, W.92, Y.117 Ligands: UNL.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.40 UNL.9: 9 residues within 4Å: Chain B: Y.18, M.22, E.40, N.90, F.97, D.99, K.115, Y.117 Ligands: UNL.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.18, B:E.40, B:D.99, B:K.115 UNL.10: 6 residues within 4Å: Chain B: E.40, M.59, C.60, W.92, K.115 Ligands: UNL.11 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.40, B:E.40 Water bridges: B:K.115 UNL.11: 8 residues within 4Å: Chain B: E.40, Y.44, L.49, N.51, W.92, Y.117 Ligands: UNL.9, UNL.10 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.40, B:N.51, B:Y.117 UNL.15: 7 residues within 4Å: Chain C: Y.18, M.22, N.90, F.97, D.99, K.115 Ligands: UNL.16 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:Y.18, C:N.90, C:K.115, C:K.115, C:K.115 UNL.16: 10 residues within 4Å: Chain C: M.22, E.40, Y.44, L.49, N.51, M.59, W.92, F.97, Y.117 Ligands: UNL.15 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.40, C:N.51, C:Y.117 Water bridges: C:Y.117 UNL.17: 13 residues within 4Å: Chain D: M.22, E.40, Y.44, L.49, N.51, F.56, M.59, C.60, W.92, F.97, K.115, Y.117 Ligands: UNL.18 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:E.40, D:E.40, D:N.51, D:K.115, D:K.115, D:Y.117 UNL.18: 10 residues within 4Å: Chain D: Y.18, M.22, E.40, N.90, W.92, F.97, D.99, K.115, Y.117 Ligands: UNL.17 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:Y.18, D:N.90, D:K.115

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

ACT.3: 4 residues within 4Å: Chain A: E.31, R.32, R.111 Ligands: EDO.8 No protein-ligand interaction detected (PLIP) ACT.4: 4 residues within 4Å: Chain A: D.91, G.94, M.95, R.96 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.94 Water bridges: A:R.96 Salt bridges: A:R.96 ACT.12: 3 residues within 4Å: Chain B: R.32, R.111 Ligands: EDO.13 4 PLIP interactions: 4 interactions with chain B Water bridges: B:S.109, B:R.111, B:R.111 Salt bridges: B:R.111

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

EDO.5: 4 residues within 4Å: Chain A: F.35, G.36, K.37 Chain B: W.50 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.37, A:K.37 EDO.6: 3 residues within 4Å: Chain A: G.36, K.37 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.37 EDO.7: 5 residues within 4Å: Chain A: G.36, S.52, R.53, D.54 Ligands: EDO.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.52, A:R.53, A:R.53, A:D.54 EDO.8: 4 residues within 4Å: Chain A: R.32, S.109, R.111 Ligands: ACT.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.32, A:S.109 Water bridges: A:R.111 EDO.13: 5 residues within 4Å: Chain B: R.32, S.109, W.110, R.111 Ligands: ACT.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.109, B:W.110 Water bridges: B:R.111 EDO.14: 4 residues within 4Å: Chain A: W.50 Chain B: F.35, G.36, K.37 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.37 Water bridges: B:G.36, B:G.36, B:R.111 EDO.19: 4 residues within 4Å: Chain C: K.37 Chain D: W.50, N.51, S.52 1 PLIP interactions: 1 interactions with chain D Water bridges: D:S.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of NTF-2 like protein of unknown function (YP_166335.1) from SILICIBACTER POMEROYI DSS-3 at 1.69 A resolution. To be published

Release Date

2009-02-24

Peptides

uncharacterized NTF-2 like protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

uncharacterized NTF-2 like protein