SMTL ID : 1ji5.1

Dlp-1 from bacillus anthracis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-12-mer

Ligands

12 x FE: FE (III) ION(Non-covalent)

FE.1: 4 residues within 4Å: Chain A: D.51, E.55 Chain B: H.24, Y.43 5 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:D.51, A:D.51, A:E.55, B:H.24, H2O.3 FE.2: 3 residues within 4Å: Chain A: H.24 Chain B: D.51, E.55 5 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: A:H.24, B:D.51, B:D.51, B:E.55, H2O.2 FE.4: 4 residues within 4Å: Chain C: D.51, E.55 Chain D: H.24, Y.43 5 PLIP interactions: 1 interactions with chain D, 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:H.24, C:D.51, C:D.51, C:E.55, H2O.6 FE.5: 4 residues within 4Å: Chain C: H.24, Y.43 Chain D: D.51, E.55 5 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: D:D.51, D:D.51, D:E.55, C:H.24, H2O.5 FE.6: 4 residues within 4Å: Chain E: D.51, E.55 Chain F: H.24, Y.43 5 PLIP interactions: 3 interactions with chain E, 1 interactions with chain F, 1 Ligand-Water interactions Metal complexes: E:D.51, E:D.51, E:E.55, F:H.24, H2O.9 FE.7: 3 residues within 4Å: Chain E: H.24 Chain F: D.51, E.55 5 PLIP interactions: 3 interactions with chain F, 1 interactions with chain E, 1 Ligand-Water interactions Metal complexes: F:D.51, F:D.51, F:E.55, E:H.24, H2O.8 FE.9: 4 residues within 4Å: Chain G: D.51, E.55 Chain H: H.24, Y.43 5 PLIP interactions: 1 interactions with chain H, 3 interactions with chain G, 1 Ligand-Water interactions Metal complexes: H:H.24, G:D.51, G:D.51, G:E.55, H2O.12 FE.10: 4 residues within 4Å: Chain G: H.24, Y.43 Chain H: D.51, E.55 5 PLIP interactions: 3 interactions with chain H, 1 interactions with chain G, 1 Ligand-Water interactions Metal complexes: H:D.51, H:D.51, H:E.55, G:H.24, H2O.10 FE.11: 4 residues within 4Å: Chain I: D.51, E.55 Chain J: H.24, Y.43 5 PLIP interactions: 3 interactions with chain I, 1 interactions with chain J, 1 Ligand-Water interactions Metal complexes: I:D.51, I:D.51, I:E.55, J:H.24, H2O.15 FE.12: 3 residues within 4Å: Chain I: H.24 Chain J: D.51, E.55 5 PLIP interactions: 3 interactions with chain J, 1 interactions with chain I, 1 Ligand-Water interactions Metal complexes: J:D.51, J:D.51, J:E.55, I:H.24, H2O.14 FE.14: 4 residues within 4Å: Chain K: D.51, E.55 Chain L: H.24, Y.43 5 PLIP interactions: 1 interactions with chain L, 3 interactions with chain K, 1 Ligand-Water interactions Metal complexes: L:H.24, K:D.51, K:D.51, K:E.55, H2O.18 FE.15: 4 residues within 4Å: Chain K: H.24, Y.43 Chain L: D.51, E.55 5 PLIP interactions: 1 interactions with chain K, 3 interactions with chain L, 1 Ligand-Water interactions Metal complexes: K:H.24, L:D.51, L:D.51, L:E.55, H2O.16

3 x MPD: (4S)-2-METHYL-2,4-PENTANEDIOL(Non-functional Binders)

MPD.3: 9 residues within 4Å: Chain A: S.14, F.17, T.18, I.50, M.68 Chain B: S.14, F.17, T.18, M.68 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.17, B:F.17, A:F.17, A:I.50 Hydrogen bonds: B:S.14, B:T.18, B:T.18 MPD.8: 9 residues within 4Å: Chain E: S.14, F.17, T.18, I.50, M.68 Chain F: S.14, F.17, T.18, M.68 7 PLIP interactions: 2 interactions with chain E, 5 interactions with chain F Hydrophobic interactions: E:F.17, E:I.50, F:F.17, F:F.17 Hydrogen bonds: F:S.14, F:T.18, F:T.18 MPD.13: 9 residues within 4Å: Chain I: S.14, F.17, T.18, I.50, M.68 Chain J: S.14, F.17, T.18, M.68 7 PLIP interactions: 2 interactions with chain I, 5 interactions with chain J Hydrophobic interactions: I:F.17, I:I.50, J:F.17, J:F.17 Hydrogen bonds: J:S.14, J:T.18, J:T.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Papinutto, E. et al., Structure of two iron-binding proteins from Bacillus anthracis. J.Biol.Chem. (2002)

Release Date

2002-06-19

Peptides

Dlp-1: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
A

F
B

G
C

H
D

I
A

J
B

K
C

L
D

Dlp-1