SMTL ID : 2p6t.1

CRYSTAL STRUCTURE OF TRANSCRIPTIONAL REGULATOR NMB0573 and L-LEUCINE COMPLEX FROM NEISSERIA MENINGITIDIS

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

homo-octamer

Ligands

8 x LEU: LEUCINE(Non-covalent)

LEU.1: 11 residues within 4Å: Chain A: L.104, T.105, G.106, T.108, D.109 Chain B: L.145 Chain G: L.127, L.131, A.139, Q.140, S.141 7 PLIP interactions: 3 interactions with chain A, 3 interactions with chain G, 1 interactions with chain B, Hydrophobic interactions: A:D.109, G:L.127, G:L.131, B:L.145 Hydrogen bonds: A:G.106, A:G.106, G:S.141 LEU.5: 12 residues within 4Å: Chain A: L.145 Chain B: L.104, T.105, G.106, T.108, D.109 Chain D: V.126, L.131, A.139, Q.140, S.141 Ligands: CA.4 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain B, Hydrophobic interactions: D:L.131 Hydrogen bonds: D:S.141, B:G.106, B:G.106 LEU.8: 11 residues within 4Å: Chain A: V.126, L.131, A.139, Q.140, S.141 Chain C: L.104, T.105, G.106, T.108, D.109 Chain D: L.145 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A, Hydrophobic interactions: C:D.109 Hydrogen bonds: C:G.106, C:G.106, A:S.141 LEU.11: 11 residues within 4Å: Chain C: L.145 Chain D: R.85, L.104, T.105, G.106, T.108, D.109 Chain F: L.131, A.139, Q.140, S.141 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: F:L.131 Hydrogen bonds: F:A.139, F:S.141, D:G.106 LEU.16: 11 residues within 4Å: Chain C: L.127, L.131, A.139, Q.140, S.141 Chain E: L.104, T.105, G.106, T.108, D.109 Chain F: L.145 8 PLIP interactions: 4 interactions with chain E, 3 interactions with chain C, 1 interactions with chain F, Hydrophobic interactions: E:D.109, C:L.127, C:L.131, F:L.145 Hydrogen bonds: E:G.106, E:G.106, E:D.109, C:S.141 LEU.19: 13 residues within 4Å: Chain E: L.145 Chain F: R.85, L.104, T.105, G.106, T.108, D.109 Chain H: V.126, L.127, A.139, Q.140, S.141 Ligands: CA.22 6 PLIP interactions: 3 interactions with chain F, 1 interactions with chain E, 2 interactions with chain H Hydrophobic interactions: F:D.109, E:L.145, H:L.127 Hydrogen bonds: F:G.106, F:G.106, H:S.141 LEU.21: 10 residues within 4Å: Chain E: L.131, A.139, Q.140, S.141 Chain G: L.104, T.105, G.106, T.108, D.109 Chain H: L.145 4 PLIP interactions: 1 interactions with chain G, 3 interactions with chain E Hydrogen bonds: G:G.106, E:A.139, E:S.141 Hydrophobic interactions: E:L.131 LEU.25: 10 residues within 4Å: Chain B: A.139, Q.140, S.141 Chain G: L.145 Chain H: R.85, L.104, T.105, G.106, T.108, D.109 5 PLIP interactions: 1 interactions with chain G, 1 interactions with chain B, 3 interactions with chain H Hydrophobic interactions: G:L.145, H:D.109 Hydrogen bonds: B:S.141, H:G.106, H:G.106

6 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: Q.17, V.18, E.21, R.33 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.17, A:R.33 GOL.9: 4 residues within 4Å: Chain C: N.120 Chain F: E.64, G.69, V.144 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.120 GOL.12: 5 residues within 4Å: Chain A: N.120 Chain D: E.64, G.69, Q.71, V.144 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.71 GOL.13: 3 residues within 4Å: Chain D: N.67, T.117, D.118 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:N.67, D:T.117 GOL.17: 2 residues within 4Å: Chain E: N.67 Ligands: GOL.18 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.67 GOL.18: 9 residues within 4Å: Chain E: L.70, T.117, D.118, M.119 Chain H: L.70, T.117, D.118, M.119 Ligands: GOL.17 1 PLIP interactions: 1 interactions with chain H Hydrogen bonds: H:T.117

11 x CA: CALCIUM ION(Non-covalent)

CA.3: 2 residues within 4Å: Chain B: N.120 Chain G: G.69 No protein-ligand interaction detected (PLIP) CA.4: 7 residues within 4Å: Chain B: G.106, E.107, T.108, D.109 Chain D: D.138, A.139 Ligands: LEU.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.109 CA.6: 2 residues within 4Å: Chain C: G.69 Chain F: N.120 3 PLIP interactions: 1 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:G.69, H2O.2, H2O.4 CA.7: 2 residues within 4Å: Chain C: D.138 Chain E: E.107 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:E.107 CA.10: 2 residues within 4Å: Chain A: G.69 Chain D: N.120 No protein-ligand interaction detected (PLIP) CA.14: 1 residues within 4Å: Chain E: G.69 No protein-ligand interaction detected (PLIP) CA.15: 3 residues within 4Å: Chain E: D.138 Chain G: E.107, D.109 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain E Metal complexes: G:E.107, E:D.138 CA.20: 2 residues within 4Å: Chain B: G.69 Chain G: N.120 No protein-ligand interaction detected (PLIP) CA.22: 6 residues within 4Å: Chain F: G.106, E.107, D.109 Chain H: D.138, A.139 Ligands: LEU.19 3 PLIP interactions: 1 interactions with chain H, 2 interactions with chain F Metal complexes: H:D.138, F:E.107, F:D.109 CA.23: 3 residues within 4Å: Chain B: D.138 Chain H: E.107, D.109 1 PLIP interactions: 1 interactions with chain H Metal complexes: H:E.107 CA.24: 1 residues within 4Å: Chain H: G.69 No protein-ligand interaction detected (PLIP)

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

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