SMTL ID : 2gyq.1

YcfI, a putative structural protein from Rhodopseudomonas palustris.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

5 x FE: FE (III) ION(Non-covalent)(Non-functional Binders)

FE.1: 6 residues within 4Å: Chain A: H.54, E.116, E.119, E.149 Ligands: ZN.4, ZN.5 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.54, A:E.119, A:E.149, H2O.5, H2O.7 FE.2: 4 residues within 4Å: Chain A: D.23, C.81, Y.118 Chain B: E.90 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Metal complexes: A:D.23, A:C.81, A:Y.118, B:E.90, B:E.90 FE.3: 4 residues within 4Å: Chain A: E.90 Chain B: D.23, C.81, Y.118 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Metal complexes: B:D.23, B:C.81, B:Y.118, A:E.90, A:E.90 FE.11: 5 residues within 4Å: Chain B: E.28, Q.61, E.119, E.149 Ligands: FE.12 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.28, B:E.28, B:E.119, B:E.149, H2O.9 FE.12: 5 residues within 4Å: Chain B: H.54, E.116, E.119, E.149 Ligands: FE.11 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.54, B:E.116, B:E.119, B:E.149, H2O.9

6 x ZN: ZINC ION(Non-covalent)(Non-functional Binders)

ZN.4: 5 residues within 4Å: Chain A: E.28, Q.61, E.119, E.149 Ligands: FE.1 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.28, A:E.28, A:E.119, A:E.149, H2O.5 ZN.5: 4 residues within 4Å: Chain A: H.54, E.116, A.152 Ligands: FE.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.54, A:E.116, H2O.2, H2O.7 ZN.6: 4 residues within 4Å: Chain A: E.93, E.97 Chain B: H.19 Ligands: ZN.7 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:H.19, A:E.97, A:E.97, H2O.1, H2O.6 ZN.7: 3 residues within 4Å: Chain A: E.97 Chain B: H.19 Ligands: ZN.6 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:H.19, A:E.97, A:E.97, H2O.6, H2O.6 ZN.13: 2 residues within 4Å: Chain A: H.19 Chain B: E.97 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:E.97, A:H.19, H2O.9, H2O.11, H2O.14 ZN.14: 4 residues within 4Å: Chain A: A.170, S.171 Chain B: E.14, H.135 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.14, B:E.14, B:H.135, H2O.4

1 x NA: SODIUM ION(Non-covalent)

NA.8: 1 residues within 4Å: Chain A: D.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.9

4 x ACT: ACETATE ION(Non-covalent)(Non-functional Binders)

ACT.9: 2 residues within 4Å: Chain A: R.64, T.144 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.64, A:R.64 Salt bridges: A:R.64 ACT.10: 5 residues within 4Å: Chain A: Q.113, H.117, N.153, N.157 Chain B: A.121 5 PLIP interactions: 1 interactions with chain B, 4 interactions with chain A Water bridges: B:G.124 Hydrophobic interactions: A:Q.113 Hydrogen bonds: A:N.153, A:N.153 Salt bridges: A:H.117 ACT.15: 4 residues within 4Å: Chain A: I.120 Chain B: H.117, N.153, N.157 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.153, B:N.157 Salt bridges: B:H.117 Hydrophobic interactions: A:I.120 ACT.16: 7 residues within 4Å: Chain B: I.31, L.35, M.38, H.54, A.112, V.115, E.116 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.31, B:L.35

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

EDO.17: 4 residues within 4Å: Chain B: R.64, R.140, F.141, T.144 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.64, B:T.144 EDO.18: 5 residues within 4Å: Chain A: A.110 Chain B: G.20, D.23, R.122, W.129 5 PLIP interactions: 2 interactions with chain A, 3 interactions with chain B Water bridges: A:E.90, A:N.111, B:R.122 Hydrogen bonds: B:D.23, B:D.23

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Osipiuk, J. et al., X-ray crystal structure of YcfI protein, a putative structural protein from Rhodopseudomonas palustris. To be Published

Release Date

2006-06-13

Peptides

ycfI, putative structural protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ycfI, putative structural protein