SMTL ID : 4nkp.2 (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

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

SO4.1: 9 residues within 4Å: Chain A: H.64, A.68, K.72, M.109, G.128, G.129, A.130, D.135 Chain G: L.102 8 PLIP interactions: 3 interactions with chain G, 5 interactions with chain A Water bridges: G:Q.79, G:Q.79, G:Q.79 Hydrogen bonds: A:G.129, A:A.130, A:D.135 Salt bridges: A:H.64, A:K.72 SO4.3: 10 residues within 4Å: Chain B: H.64, A.68, K.72, M.109, G.128, G.129, A.130, H.131, D.135 Chain F: L.102 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain F Hydrogen bonds: B:G.129, B:A.130, B:H.131, B:D.135 Water bridges: B:H.64, F:Q.79 Salt bridges: B:H.64, B:K.72 SO4.6: 9 residues within 4Å: Chain C: H.64, A.68, K.72, M.109, G.128, G.129, A.130, D.135 Chain E: L.102 8 PLIP interactions: 3 interactions with chain E, 5 interactions with chain C Water bridges: E:Q.79, E:Q.79, E:Q.79 Hydrogen bonds: C:G.129, C:A.130, C:D.135 Salt bridges: C:H.64, C:K.72 SO4.8: 10 residues within 4Å: Chain D: H.64, A.68, K.72, M.109, G.128, G.129, A.130, H.131, D.135 Chain H: L.102 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain H Hydrogen bonds: D:G.129, D:A.130, D:H.131, D:D.135 Water bridges: D:H.64, H:Q.79 Salt bridges: D:H.64, D:K.72 SO4.11: 9 residues within 4Å: Chain A: L.102 Chain E: H.64, A.68, K.72, M.109, G.128, G.129, A.130, D.135 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain E Water bridges: A:Q.79, A:Q.79, A:Q.79 Hydrogen bonds: E:G.129, E:A.130, E:D.135 Salt bridges: E:H.64, E:K.72 SO4.13: 10 residues within 4Å: Chain D: L.102 Chain F: H.64, A.68, K.72, M.109, G.128, G.129, A.130, H.131, D.135 8 PLIP interactions: 7 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:G.129, F:A.130, F:H.131, F:D.135 Water bridges: F:H.64, D:Q.79 Salt bridges: F:H.64, F:K.72 SO4.16: 9 residues within 4Å: Chain C: L.102 Chain G: H.64, A.68, K.72, M.109, G.128, G.129, A.130, D.135 8 PLIP interactions: 5 interactions with chain G, 3 interactions with chain C Hydrogen bonds: G:G.129, G:A.130, G:D.135 Salt bridges: G:H.64, G:K.72 Water bridges: C:Q.79, C:Q.79, C:Q.79 SO4.18: 10 residues within 4Å: Chain B: L.102 Chain H: H.64, A.68, K.72, M.109, G.128, G.129, A.130, H.131, D.135 8 PLIP interactions: 7 interactions with chain H, 1 interactions with chain B Hydrogen bonds: H:G.129, H:A.130, H:H.131, H:D.135 Water bridges: H:H.64, B:Q.79 Salt bridges: H:H.64, H:K.72

12 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 5 residues within 4Å: Chain A: I.52, L.66, N.67, Y.70 Ligands: GOL.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.66 Water bridges: A:N.67, A:N.67, A:N.67, A:N.67 GOL.4: 4 residues within 4Å: Chain B: I.52, N.67, Y.70 Ligands: GOL.2 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.67 GOL.5: 9 residues within 4Å: Chain B: R.48, A.77, S.78, K.80 Chain H: R.57, H.59, H.60, A.61, G.62 7 PLIP interactions: 3 interactions with chain H, 4 interactions with chain B Hydrogen bonds: H:R.57, H:H.59, B:A.77, B:K.80 Water bridges: H:V.63, B:S.49, B:V.121 GOL.7: 5 residues within 4Å: Chain C: I.52, L.66, N.67, Y.70 Ligands: GOL.9 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:L.66 Water bridges: C:N.67, C:N.67, C:N.67, C:N.67 GOL.9: 4 residues within 4Å: Chain D: I.52, N.67, Y.70 Ligands: GOL.7 1 PLIP interactions: 1 interactions with chain D Water bridges: D:N.67 GOL.10: 9 residues within 4Å: Chain D: R.48, A.77, S.78, K.80 Chain F: R.57, H.59, H.60, A.61, G.62 7 PLIP interactions: 4 interactions with chain D, 3 interactions with chain F Hydrogen bonds: D:A.77, D:K.80, F:R.57, F:H.59 Water bridges: D:S.49, D:V.121, F:V.63 GOL.12: 5 residues within 4Å: Chain E: I.52, L.66, N.67, Y.70 Ligands: GOL.14 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:L.66 Water bridges: E:N.67, E:N.67, E:N.67, E:N.67 GOL.14: 4 residues within 4Å: Chain F: I.52, N.67, Y.70 Ligands: GOL.12 1 PLIP interactions: 1 interactions with chain F Water bridges: F:N.67 GOL.15: 9 residues within 4Å: Chain B: R.57, H.59, H.60, A.61, G.62 Chain F: R.48, A.77, S.78, K.80 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain F Hydrogen bonds: B:R.57, B:H.59, F:A.77, F:K.80 Water bridges: B:V.63, F:S.49, F:V.121 GOL.17: 5 residues within 4Å: Chain G: I.52, L.66, N.67, Y.70 Ligands: GOL.19 5 PLIP interactions: 5 interactions with chain G Hydrogen bonds: G:L.66 Water bridges: G:N.67, G:N.67, G:N.67, G:N.67 GOL.19: 4 residues within 4Å: Chain H: I.52, N.67, Y.70 Ligands: GOL.17 1 PLIP interactions: 1 interactions with chain H Water bridges: H:N.67 GOL.20: 9 residues within 4Å: Chain D: R.57, H.59, H.60, A.61, G.62 Chain H: R.48, A.77, S.78, K.80 7 PLIP interactions: 4 interactions with chain H, 3 interactions with chain D Hydrogen bonds: H:A.77, H:K.80, D:R.57, D:H.59 Water bridges: H:S.49, H:V.121, D:V.63

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
C

B
D

C
C

D
D

E
C

F
D

G
C

H
D

putative extracellular heme-binding protein

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