SMTL ID : 3dza.1

Crystal structure of a putative membrane protein of unknown function (yfdx) from klebsiella pneumoniae subsp. at 1.65 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-tetramer

Ligands

10 x ZN: ZINC ION(Non-covalent)

ZN.1: 2 residues within 4Å: Chain A: H.48 Chain B: E.140 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: A:H.48, B:E.140, H2O.14, H2O.15, H2O.15, H2O.16 ZN.2: 2 residues within 4Å: Chain A: E.140 Chain B: H.48 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: B:H.48, A:E.140, H2O.2, H2O.3, H2O.3, H2O.13 ZN.3: 2 residues within 4Å: Chain A: D.183 Chain D: D.183 6 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: A:D.183, D:D.183, H2O.3, H2O.3, H2O.35, H2O.35 ZN.9: 1 residues within 4Å: Chain B: E.109 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.109, B:E.109, H2O.15, H2O.16, H2O.21 ZN.10: 2 residues within 4Å: Chain B: D.183 Chain C: D.183 6 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: C:D.183, B:D.183, H2O.13, H2O.14, H2O.14, H2O.24 ZN.20: 3 residues within 4Å: Chain C: H.48 Chain D: E.140 Ligands: EDO.35 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:H.48, D:E.140, H2O.34, H2O.35 ZN.21: 2 residues within 4Å: Chain C: D.79, E.185 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.79, C:E.185, C:E.185, H2O.30, H2O.31 ZN.22: 2 residues within 4Å: Chain C: Q.113, E.117 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:E.117, C:E.117, H2O.29 ZN.23: 3 residues within 4Å: Chain C: E.140 Chain D: H.48 Ligands: EDO.27 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: C:E.140, D:H.48, H2O.25, H2O.25 ZN.29: 1 residues within 4Å: Chain D: E.109 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:E.109, D:E.109, H2O.37, H2O.40

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

EDO.4: 5 residues within 4Å: Chain A: Y.143, E.177, I.180, V.182 Ligands: EDO.8 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: Q.31, A.67, S.71, W.72, F.75 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: Q.149, K.152, A.153, Q.156, V.172 Chain D: D.101 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: A.120, K.121, G.122 Chain B: G.49, P.51, D.52 Ligands: ACT.11 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: A.33, I.92, N.93 Ligands: EDO.4 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain B: A.33, I.92, N.93 Ligands: EDO.19 Ligand excluded by PLIP EDO.14: 5 residues within 4Å: Chain B: Q.31, A.67, S.71, W.72, F.75 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain B: M.186 Chain C: A.80, K.81 Ligands: EDO.16 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain B: R.132, M.186 Chain C: K.83, I.85 Ligands: EDO.15 Ligand excluded by PLIP EDO.17: 3 residues within 4Å: Chain A: Q.40 Chain B: N.93, Y.143 Ligand excluded by PLIP EDO.18: 2 residues within 4Å: Chain A: S.95 Chain B: Q.40 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain B: Y.143, E.177, I.180, V.182 Ligands: EDO.13 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain C: A.33, I.92, N.93 Ligand excluded by PLIP EDO.26: 5 residues within 4Å: Chain C: Q.31, A.67, S.71, W.72, F.75 Ligand excluded by PLIP EDO.27: 7 residues within 4Å: Chain C: L.26, V.28, I.91, E.140, Q.142 Chain D: H.48 Ligands: ZN.23 Ligand excluded by PLIP EDO.28: 6 residues within 4Å: Chain B: D.101 Chain C: Q.149, K.152, A.153, Q.156, V.172 Ligand excluded by PLIP EDO.32: 1 residues within 4Å: Chain D: E.177 Ligand excluded by PLIP EDO.33: 6 residues within 4Å: Chain D: K.20, Q.31, A.67, S.71, W.72, F.75 Ligand excluded by PLIP EDO.34: 3 residues within 4Å: Chain A: K.83, A.86 Chain D: R.132 Ligand excluded by PLIP EDO.35: 6 residues within 4Å: Chain C: H.48 Chain D: L.26, V.28, E.140, Q.142 Ligands: ZN.20 Ligand excluded by PLIP EDO.36: 5 residues within 4Å: Chain A: D.101 Chain D: Q.149, A.153, Q.156, V.172 Ligand excluded by PLIP EDO.37: 3 residues within 4Å: Chain C: Q.40 Chain D: N.93, Y.143 Ligand excluded by PLIP EDO.38: 3 residues within 4Å: Chain D: A.33, I.92, N.93 Ligand excluded by PLIP EDO.39: 3 residues within 4Å: Chain A: R.132, M.186 Chain D: A.86 Ligand excluded by PLIP

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

ACT.11: 5 residues within 4Å: Chain B: Q.50, P.51, D.52, S.53 Ligands: EDO.7 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.52, B:S.53 ACT.12: 4 residues within 4Å: Chain A: T.16, N.34 Chain B: T.16, N.34 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Water bridges: A:T.16, A:T.16, A:N.34, B:T.16, B:N.34, B:N.34 ACT.24: 4 residues within 4Å: Chain C: Q.50, P.51, D.52, S.53 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.52, C:S.53 ACT.30: 7 residues within 4Å: Chain C: T.16, Q.19, N.34, R.37 Chain D: T.16, N.34, R.37 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain C Hydrogen bonds: D:N.34 Water bridges: D:T.16, D:N.34, D:R.37, C:T.16, C:T.16, C:R.37 ACT.31: 4 residues within 4Å: Chain D: Q.50, P.51, D.52, S.53 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:D.52, D:S.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of putative membrane protein of unknown function (YP_001337144.1) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.65 A resolution. To be published

Release Date

2008-08-12

Peptides

uncharacterized putative membrane protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

uncharacterized putative membrane protein