SMTL ID : 1t35.1

CRYSTAL STRUCTURE OF A HYPOTHETICAL PROTEIN YVDD- A PUTATIVE LYSINE DECARBOXYLASE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.72 Å

Oligo State

homo-octamer

Ligands

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

SO4.1: 9 residues within 4Å: Chain A: G.9, S.10, G.106, G.107, F.108, G.109, T.110 Chain E: G.71, H.75 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:S.10, A:G.107, A:G.109, A:T.110 Salt bridges: E:H.75 SO4.2: 4 residues within 4Å: Chain A: G.86, M.87, H.88 Chain B: H.88 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 1 interactions with chain E Hydrogen bonds: A:H.88, E:S.66 Salt bridges: B:H.88 SO4.3: 8 residues within 4Å: Chain B: A.8, G.9, S.10, G.106, G.107, F.108, G.109, T.110 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.10, B:G.107, B:G.109, B:T.110, B:T.110 SO4.4: 7 residues within 4Å: Chain C: A.8, G.9, S.10, G.107, F.108, G.109, T.110 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:S.10, C:S.10, C:G.107, C:G.107, C:G.109, C:T.110 Water bridges: C:N.11 SO4.5: 10 residues within 4Å: Chain D: G.9, S.10, G.106, G.107, F.108, G.109, T.110 Chain G: G.71, V.74, H.75 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain G Hydrogen bonds: D:S.10, D:S.10, D:G.107, D:G.107, D:G.109, D:T.110, D:T.110 Salt bridges: G:H.75 SO4.6: 4 residues within 4Å: Chain C: H.88 Chain D: G.86, M.87, H.88 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Salt bridges: C:H.88 Hydrogen bonds: D:H.88 SO4.7: 11 residues within 4Å: Chain D: P.65, S.66, G.67, V.84, N.85, G.86 Chain G: P.65, S.66, G.67, V.84, G.86 6 PLIP interactions: 3 interactions with chain G, 3 interactions with chain D Hydrogen bonds: G:S.66, G:G.67, G:G.86, D:S.66, D:G.67, D:G.86 SO4.8: 10 residues within 4Å: Chain A: G.71, V.74, H.75 Chain E: G.9, S.10, G.106, G.107, F.108, G.109, T.110 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain A Hydrogen bonds: E:S.10, E:G.107, E:G.109, E:T.110, E:T.110, A:G.71 Salt bridges: A:H.75 SO4.9: 4 residues within 4Å: Chain E: G.86, M.87, H.88 Chain F: H.88 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Hydrogen bonds: F:H.88, E:H.88 SO4.10: 12 residues within 4Å: Chain A: P.65, S.66, G.67, V.84, N.85, G.86 Chain E: P.65, S.66, G.67, V.84, N.85, G.86 8 PLIP interactions: 4 interactions with chain E, 4 interactions with chain A Hydrogen bonds: E:S.66, E:G.67, E:V.84, E:G.86, A:S.66, A:G.67, A:V.84, A:G.86 SO4.11: 7 residues within 4Å: Chain F: G.9, S.10, G.106, G.107, F.108, G.109, T.110 9 PLIP interactions: 8 interactions with chain F, 1 interactions with chain H Hydrogen bonds: F:S.10, F:S.10, F:G.107, F:G.107, F:G.109, F:T.110, F:T.110 Water bridges: F:F.108, H:G.71 SO4.12: 11 residues within 4Å: Chain D: G.71, V.74, H.75 Chain G: A.8, G.9, S.10, G.106, G.107, F.108, G.109, T.110 7 PLIP interactions: 5 interactions with chain G, 2 interactions with chain D Hydrogen bonds: G:S.10, G:G.107, G:G.109, G:T.110, G:T.110, D:G.71 Salt bridges: D:H.75 SO4.13: 4 residues within 4Å: Chain G: G.86, M.87, H.88 Chain H: H.88 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain H Hydrogen bonds: G:H.88, H:H.88 SO4.14: 9 residues within 4Å: Chain G: F.154 Chain H: A.8, G.9, S.10, G.106, G.107, F.108, G.109, T.110 7 PLIP interactions: 2 interactions with chain F, 5 interactions with chain H Water bridges: F:S.70, F:G.71 Hydrogen bonds: H:S.10, H:G.107, H:G.109, H:T.110, H:T.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rajashankar, K.R. et al., Crystal Structure of a Hypothetical Protein Yvdd - Putative Lysine Decarboxylase. To be Published

Release Date

2004-05-04

Peptides

HYPOTHETICAL PROTEIN YVDD, Putative Lysine Decarboxylase: ABCDEFGH

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

HYPOTHETICAL PROTEIN YVDD, Putative Lysine Decarboxylase