SMTL ID : 4nkp.1 (1 other biounit)

Crystal structure of a putative extracellular heme-binding protein (DESPIG_02683) from Desulfovibrio piger ATCC 29098 at 1.24 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.24 Å

Oligo State

homo-octamer

Ligands

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

SO4.1: 10 residues within 4Å: Chain A: H.64, A.68, K.72, M.109, G.128, G.129, A.130, H.131, D.135 Chain E: L.102 11 PLIP interactions: 2 interactions with chain E, 9 interactions with chain A Water bridges: E:Q.79, E:Q.79, A:H.131, A:H.131, A:H.131 Hydrogen bonds: A:G.129, A:A.130, A:H.131, A:D.135 Salt bridges: A:H.64, A:K.72 SO4.6: 10 residues within 4Å: Chain C: H.64, A.68, K.72, M.109, G.128, G.129, A.130, H.131, D.135 Chain G: L.102 11 PLIP interactions: 9 interactions with chain C, 2 interactions with chain G Hydrogen bonds: C:G.129, C:A.130, C:H.131, C:D.135 Water bridges: C:H.131, C:H.131, C:H.131, G:Q.79, G:Q.79 Salt bridges: C:H.64, C:K.72 SO4.11: 10 residues within 4Å: Chain C: L.102 Chain E: H.64, A.68, K.72, M.109, G.128, G.129, A.130, H.131, D.135 11 PLIP interactions: 9 interactions with chain E, 2 interactions with chain C Hydrogen bonds: E:G.129, E:A.130, E:H.131, E:D.135 Water bridges: E:H.131, E:H.131, E:H.131, C:Q.79, C:Q.79 Salt bridges: E:H.64, E:K.72 SO4.16: 10 residues within 4Å: Chain A: L.102 Chain G: H.64, A.68, K.72, M.109, G.128, G.129, A.130, H.131, D.135 11 PLIP interactions: 9 interactions with chain G, 2 interactions with chain A Hydrogen bonds: G:G.129, G:A.130, G:H.131, G:D.135 Water bridges: G:H.131, G:H.131, G:H.131, A:Q.79, A:Q.79 Salt bridges: G:H.64, G:K.72

16 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: I.52, N.67, Y.70 Ligands: GOL.5 Ligand excluded by PLIP GOL.3: 9 residues within 4Å: Chain B: R.48, A.77, S.78, K.80 Chain F: R.57, H.59, H.60, A.61, G.62 Ligand excluded by PLIP GOL.4: 11 residues within 4Å: Chain B: L.102 Chain F: H.64, T.65, A.68, K.72, M.109, G.128, G.129, A.130, H.131, D.135 Ligand excluded by PLIP GOL.5: 5 residues within 4Å: Chain B: I.52, L.66, N.67, Y.70 Ligands: GOL.2 Ligand excluded by PLIP GOL.7: 4 residues within 4Å: Chain C: I.52, N.67, Y.70 Ligands: GOL.10 Ligand excluded by PLIP GOL.8: 9 residues within 4Å: Chain D: R.48, A.77, S.78, K.80 Chain H: R.57, H.59, H.60, A.61, G.62 Ligand excluded by PLIP GOL.9: 11 residues within 4Å: Chain D: L.102 Chain H: H.64, T.65, A.68, K.72, M.109, G.128, G.129, A.130, H.131, D.135 Ligand excluded by PLIP GOL.10: 5 residues within 4Å: Chain D: I.52, L.66, N.67, Y.70 Ligands: GOL.7 Ligand excluded by PLIP GOL.12: 4 residues within 4Å: Chain E: I.52, N.67, Y.70 Ligands: GOL.15 Ligand excluded by PLIP GOL.13: 9 residues within 4Å: Chain D: R.57, H.59, H.60, A.61, G.62 Chain F: R.48, A.77, S.78, K.80 Ligand excluded by PLIP GOL.14: 11 residues within 4Å: Chain D: H.64, T.65, A.68, K.72, M.109, G.128, G.129, A.130, H.131, D.135 Chain F: L.102 Ligand excluded by PLIP GOL.15: 5 residues within 4Å: Chain F: I.52, L.66, N.67, Y.70 Ligands: GOL.12 Ligand excluded by PLIP GOL.17: 4 residues within 4Å: Chain G: I.52, N.67, Y.70 Ligands: GOL.20 Ligand excluded by PLIP GOL.18: 9 residues within 4Å: Chain B: R.57, H.59, H.60, A.61, G.62 Chain H: R.48, A.77, S.78, K.80 Ligand excluded by PLIP GOL.19: 11 residues within 4Å: Chain B: H.64, T.65, A.68, K.72, M.109, G.128, G.129, A.130, H.131, D.135 Chain H: L.102 Ligand excluded by PLIP GOL.20: 5 residues within 4Å: Chain H: I.52, L.66, N.67, Y.70 Ligands: GOL.17 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 (DESPIG_02683) from Desulfovibrio piger ATCC 29098 at 1.24 A resolution. To be published

Release Date

2013-12-11

Peptides

putative extracellular heme-binding protein: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

E
A

F
B

G
A

H
B

putative extracellular heme-binding protein

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