SMTL ID : 4hyz.1

Crystal structure of a DUF3887 family protein (RUMGNA_01855) from Ruminococcus gnavus ATCC 29149 at 2.25 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-tetramer

Ligands

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 4 residues within 4Å: Chain A: G.1, K.78, D.79 Chain C: N.96 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain A Hydrogen bonds: C:N.96, A:G.1, A:D.79 Water bridges: A:G.1, A:G.1 SO4.2: 5 residues within 4Å: Chain A: T.40, K.41, D.104, D.106, N.108 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:K.41, A:D.106, A:D.106, A:N.108 Water bridges: A:T.40, A:D.42 SO4.9: 5 residues within 4Å: Chain A: K.13, Y.73 Chain B: K.13 Chain C: K.5 Chain D: K.5 7 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D, 2 interactions with chain B, 2 interactions with chain A Salt bridges: C:K.5, D:K.5, B:K.13, A:K.13 Water bridges: D:K.5, B:C.71 Hydrogen bonds: A:Y.73 SO4.10: 5 residues within 4Å: Chain B: G.1, I.77, K.78, D.79 Chain D: N.96 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:G.1, B:D.79, D:N.96 Water bridges: B:Q.76, B:N.80 SO4.11: 4 residues within 4Å: Chain A: K.13 Chain B: R.17, C.71, Y.73 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:C.71, B:Y.73 Salt bridges: B:R.17, A:K.13 Water bridges: A:K.13 SO4.12: 6 residues within 4Å: Chain B: T.40, K.41, D.42, D.104, D.106, N.108 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.41, B:D.42, B:D.106, B:N.108 SO4.21: 4 residues within 4Å: Chain A: N.96 Chain C: G.1, K.78, D.79 5 PLIP interactions: 1 interactions with chain A, 4 interactions with chain C Hydrogen bonds: A:N.96, C:G.1, C:D.79 Water bridges: C:G.1, C:G.1 SO4.22: 5 residues within 4Å: Chain C: T.40, K.41, D.104, D.106, N.108 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.41, C:D.106, C:N.108 Water bridges: C:D.42 SO4.29: 5 residues within 4Å: Chain A: K.5 Chain B: K.5 Chain C: K.13, Y.73 Chain D: K.13 7 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 2 interactions with chain D, 2 interactions with chain B Hydrogen bonds: C:Y.73 Salt bridges: C:K.13, A:K.5, D:K.13, B:K.5 Water bridges: D:C.71, B:K.5 SO4.30: 5 residues within 4Å: Chain B: N.96 Chain D: G.1, I.77, K.78, D.79 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain B Hydrogen bonds: D:G.1, D:D.79, B:N.96 Water bridges: D:Q.76, D:N.80 SO4.31: 4 residues within 4Å: Chain C: K.13 Chain D: R.17, C.71, Y.73 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Water bridges: C:K.13 Salt bridges: C:K.13, D:R.17 Hydrogen bonds: D:C.71 SO4.32: 6 residues within 4Å: Chain D: T.40, K.41, D.42, D.104, D.106, N.108 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.41, D:D.42, D:N.108

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

CL.3: 3 residues within 4Å: Chain A: E.9, G.10 Chain B: K.70 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: D.12, K.13 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: E.9, G.10 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: D.12, K.13 Ligands: GOL.7 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain B: T.48, E.49, E.50 Ligand excluded by PLIP CL.16: 1 residues within 4Å: Chain B: N.98 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain C: E.9, G.10 Chain D: K.70 Ligand excluded by PLIP CL.24: 2 residues within 4Å: Chain C: D.12, K.13 Ligand excluded by PLIP CL.33: 2 residues within 4Å: Chain D: E.9, G.10 Ligand excluded by PLIP CL.34: 3 residues within 4Å: Chain D: D.12, K.13 Ligands: GOL.27 Ligand excluded by PLIP CL.35: 3 residues within 4Å: Chain D: T.48, E.49, E.50 Ligand excluded by PLIP CL.36: 1 residues within 4Å: Chain D: N.98 Ligand excluded by PLIP

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: K.81, K.82, E.105 Ligand excluded by PLIP GOL.6: 3 residues within 4Å: Chain A: M.21, E.22, E.25 Ligand excluded by PLIP GOL.7: 4 residues within 4Å: Chain A: K.70, C.71, Y.73 Ligands: CL.14 Ligand excluded by PLIP GOL.8: 4 residues within 4Å: Chain A: Y.32, L.47, T.48, E.49 Ligand excluded by PLIP GOL.17: 5 residues within 4Å: Chain B: G.75, Q.76, Y.83, G.85, A.102 Ligand excluded by PLIP GOL.18: 4 residues within 4Å: Chain B: K.81, K.82, E.105, D.106 Ligand excluded by PLIP GOL.19: 2 residues within 4Å: Chain B: I.58, Q.62 Ligand excluded by PLIP GOL.20: 5 residues within 4Å: Chain B: Q.19, R.38, D.106, M.107, N.108 Ligand excluded by PLIP GOL.25: 3 residues within 4Å: Chain C: K.81, K.82, E.105 Ligand excluded by PLIP GOL.26: 3 residues within 4Å: Chain C: M.21, E.22, E.25 Ligand excluded by PLIP GOL.27: 4 residues within 4Å: Chain C: K.70, C.71, Y.73 Ligands: CL.34 Ligand excluded by PLIP GOL.28: 4 residues within 4Å: Chain C: Y.32, L.47, T.48, E.49 Ligand excluded by PLIP GOL.37: 5 residues within 4Å: Chain D: G.75, Q.76, Y.83, G.85, A.102 Ligand excluded by PLIP GOL.38: 4 residues within 4Å: Chain D: K.81, K.82, E.105, D.106 Ligand excluded by PLIP GOL.39: 2 residues within 4Å: Chain D: I.58, Q.62 Ligand excluded by PLIP GOL.40: 5 residues within 4Å: Chain D: Q.19, R.38, D.106, M.107, N.108 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Joint Center for Structural Genomics (JCSG), Crystal structure of a hypothetical protein (RUMGNA_01855) from Ruminococcus gnavus ATCC 29149 at 2.25 A resolution. To be published

Release Date

2013-01-09

Peptides

Uncharacterized protein: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Uncharacterized protein

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