SMTL ID : 2p5v.1

Crystal Structure of Transcriptional Regulator NMB0573 from Neisseria Meningitidis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-octamer

Ligands

8 x CA: CALCIUM ION(Non-covalent)

CA.1: 3 residues within 4Å: Chain A: E.107, D.109 Chain G: D.138 3 PLIP interactions: 1 interactions with chain G, 2 interactions with chain A Metal complexes: G:D.138, A:E.107, A:D.109 CA.5: 3 residues within 4Å: Chain B: E.107, D.109 Chain D: D.138 5 PLIP interactions: 2 interactions with chain B, 1 interactions with chain D, 2 Ligand-Water interactions Metal complexes: B:E.107, B:D.109, D:D.138, H2O.7, H2O.14 CA.9: 3 residues within 4Å: Chain A: D.138 Chain C: E.107, D.109 4 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: C:E.107, C:D.109, A:D.138, H2O.1 CA.10: 3 residues within 4Å: Chain C: D.138 Chain E: E.107, D.109 5 PLIP interactions: 2 interactions with chain E, 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: E:E.107, E:D.109, C:D.138, H2O.13, H2O.17 CA.13: 3 residues within 4Å: Chain D: E.107, D.109 Chain F: D.138 5 PLIP interactions: 2 interactions with chain D, 1 interactions with chain F, 2 Ligand-Water interactions Metal complexes: D:E.107, D:D.109, F:D.138, H2O.16, H2O.21 CA.21: 3 residues within 4Å: Chain F: E.107, D.109 Chain H: D.138 5 PLIP interactions: 1 interactions with chain F, 1 interactions with chain H, 3 Ligand-Water interactions Metal complexes: F:E.107, H:D.138, H2O.23, H2O.23, H2O.24 CA.24: 3 residues within 4Å: Chain E: D.138 Chain G: E.107, D.109 3 PLIP interactions: 1 interactions with chain E, 2 interactions with chain G Metal complexes: E:D.138, G:E.107, G:D.109 CA.26: 3 residues within 4Å: Chain B: D.138 Chain H: E.107, D.109 5 PLIP interactions: 1 interactions with chain B, 2 interactions with chain H, 2 Ligand-Water interactions Metal complexes: B:D.138, H:E.107, H:D.109, H2O.5, H2O.28

10 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 4 residues within 4Å: Chain A: D.118, M.119 Chain D: D.118, M.119 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain B: D.118, M.119 Chain G: D.118, M.119 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: K.146 Chain B: R.85, Y.110 Ligand excluded by PLIP CL.11: 4 residues within 4Å: Chain C: D.118, M.119 Chain F: D.118, M.119 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain A: L.127 Chain C: R.85, Y.110 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain C: K.146 Chain D: R.85, Y.110 Ligand excluded by PLIP CL.16: 6 residues within 4Å: Chain E: N.22, G.23, R.24, L.25 Chain F: Y.57 Ligands: CL.22 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain E: D.118, M.119 Chain H: D.118, M.119 Ligand excluded by PLIP CL.22: 4 residues within 4Å: Chain E: E.21 Chain F: Q.56, Y.57 Ligands: CL.16 Ligand excluded by PLIP CL.23: 5 residues within 4Å: Chain E: Y.57 Chain F: N.22, G.23, R.24, L.25 Ligand excluded by PLIP

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: M.119, N.120, S.123 Chain D: G.69, V.144, L.145 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:V.144, A:N.120, A:S.123 Water bridges: D:E.147 GOL.4: 6 residues within 4Å: Chain A: Q.5, L.6, L.8, L.159 Chain B: S.65, N.67 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.5, A:L.6 Water bridges: A:L.8 GOL.8: 3 residues within 4Å: Chain B: E.64, G.69 Chain G: N.120 5 PLIP interactions: 3 interactions with chain G, 2 interactions with chain B Hydrogen bonds: G:N.120, G:N.120, B:E.64 Water bridges: G:N.120, B:G.69 GOL.15: 8 residues within 4Å: Chain C: F.73, R.75, L.111, S.142 Chain D: R.75, L.104, T.108, L.111 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:S.142, C:S.142, D:R.75, D:T.108 Water bridges: D:T.108 GOL.18: 5 residues within 4Å: Chain E: R.75, Q.140, S.141, S.142 Chain F: G.106 7 PLIP interactions: 1 interactions with chain H, 1 interactions with chain G, 5 interactions with chain E Water bridges: H:S.141, G:T.105, E:R.75, E:T.108, E:S.141, E:S.142, E:S.142 GOL.19: 3 residues within 4Å: Chain E: N.120 Chain H: E.64, G.69 6 PLIP interactions: 2 interactions with chain E, 4 interactions with chain H Water bridges: E:N.120, E:S.123, H:L.145 Hydrogen bonds: H:E.64, H:E.64, H:G.69 GOL.20: 2 residues within 4Å: Chain E: G.69 Chain H: N.120 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain E Water bridges: H:S.123 Hydrogen bonds: E:L.145 GOL.25: 3 residues within 4Å: Chain B: N.120 Chain G: E.64, G.69 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain G Hydrogen bonds: B:N.120, B:N.120, G:E.64 Water bridges: B:S.123

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ren, J. et al., The Structure and Transcriptional Analysis of a Global Regulator from Neisseria meningitidis. J.Biol.Chem. (2007)

Release Date

2007-04-03

Peptides

Transcriptional regulator, LRP/AsnC family: 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

Transcriptional regulator, LRP/AsnC family

Related Entries With Identical Sequence