SMTL ID : 3onr.1

Crystal structure of the calcium chelating immunodominant antigen, calcium dodecin (Rv0379),from Mycobacterium tuberculosis with a novel calcium-binding site

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-12-mer

Ligands

4 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: E.19 Chain B: E.19 Chain C: E.19 5 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: C:E.19, A:E.19, A:E.19, H2O.1, H2O.2 CA.5: 3 residues within 4Å: Chain D: E.19 Chain E: E.19 Chain F: E.19 5 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: F:E.19, E:E.19, D:E.19, H2O.4, H2O.5 CA.11: 3 residues within 4Å: Chain G: E.19 Chain H: E.19 Chain I: E.19 5 PLIP interactions: 2 interactions with chain H, 2 interactions with chain G, 1 interactions with chain I Metal complexes: H:E.19, H:E.19, G:E.19, G:E.19, I:E.19 CA.16: 3 residues within 4Å: Chain J: E.19 Chain K: E.19 Chain L: E.19 5 PLIP interactions: 1 interactions with chain J, 1 interactions with chain K, 1 interactions with chain L, 2 Ligand-Water interactions Metal complexes: J:E.19, K:E.19, L:E.19, H2O.13, H2O.14

12 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 4 residues within 4Å: Chain A: I.11, E.43, D.45, R.57 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.43, A:R.57 FMT.3: 3 residues within 4Å: Chain B: E.43, D.45, R.57 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.57, B:K.59 FMT.4: 5 residues within 4Å: Chain C: I.11, E.43, D.45, R.57, K.59 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.57, C:K.59 FMT.6: 4 residues within 4Å: Chain D: E.43, D.45, R.57, K.59 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:E.43 FMT.7: 3 residues within 4Å: Chain E: E.43, D.45, R.57 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:R.57 FMT.9: 3 residues within 4Å: Chain F: E.43, D.45, R.57 2 PLIP interactions: 2 interactions with chain F Hydrogen bonds: F:R.57, F:R.57 FMT.12: 4 residues within 4Å: Chain G: E.43, D.45, R.57, K.59 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:E.43 FMT.13: 5 residues within 4Å: Chain H: I.11, E.43, D.45, R.57, K.59 2 PLIP interactions: 2 interactions with chain H Hydrogen bonds: H:E.43, H:K.59 FMT.14: 3 residues within 4Å: Chain I: E.43, D.45, R.57 2 PLIP interactions: 2 interactions with chain I Hydrogen bonds: I:E.43, I:E.43 FMT.17: 4 residues within 4Å: Chain J: E.43, D.45, R.57, K.59 3 PLIP interactions: 3 interactions with chain J Hydrogen bonds: J:R.57, J:K.59 Water bridges: J:K.59 FMT.18: 3 residues within 4Å: Chain K: E.43, D.45, R.57 1 PLIP interactions: 1 interactions with chain K Hydrogen bonds: K:R.57 FMT.19: 3 residues within 4Å: Chain L: E.43, D.45, R.57 3 PLIP interactions: 3 interactions with chain L Hydrogen bonds: L:E.43, L:E.43, L:R.57

3 x PT: PLATINUM (II) ION(Non-covalent)(Non-functional Binders)

PT.8: 1 residues within 4Å: Chain E: P.68 No protein-ligand interaction detected (PLIP) PT.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) PT.15: 1 residues within 4Å: Chain I: R.67 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arockiasamy, A. et al., Crystal structure of calcium dodecin (Rv0379), from Mycobacterium tuberculosis with a unique calcium-binding site. Protein Sci. (2011)

Release Date

2011-03-16

Peptides

PROTEIN TRANSPORT PROTEIN SECE2: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

PROTEIN TRANSPORT PROTEIN SECE2