SMTL ID : 6jdb.1

Crystal structure of N-acetyl mannosmaine kinase in complex with ManNAc-6P and ADP from Haemophilus influenzae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-dimer

Ligands

2 x ADP: ADENOSINE-5'-DIPHOSPHATE(Non-covalent)

ADP.1: 12 residues within 4Å: Chain A: G.9, G.10, T.11, K.12, S.129, T.130, G.179, P.195, K.196, S.241, V.242 Ligands: BMX.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:G.10, A:T.11, A:K.12, A:S.129, A:T.130, A:T.130, A:K.196, A:S.241, A:S.241, A:Q.274 Water bridges: A:D.7, A:K.12 Salt bridges: A:K.12, A:K.12 ADP.4: 12 residues within 4Å: Chain B: G.9, G.10, T.11, K.12, S.129, T.130, G.179, P.195, K.196, S.241, V.242 Ligands: BMX.5 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:G.10, B:T.11, B:K.12, B:S.129, B:T.130, B:T.130, B:K.196, B:S.241, B:S.241, B:Q.274 Water bridges: B:D.7, B:K.12 Salt bridges: B:K.12, B:K.12

2 x BMX: 2-acetamido-2-deoxy-6-O-phosphono-alpha-D-mannopyranose(Non-covalent)

BMX.2: 20 residues within 4Å: Chain A: G.9, G.10, T.62, G.63, A.72, L.73, N.74, N.77, N.102, D.103, A.104, S.129, T.130, G.131, V.132, G.133, H.152, H.155, E.174 Ligands: ADP.1 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:A.72 Hydrogen bonds: A:G.10, A:T.62, A:T.62, A:G.63, A:N.74, A:N.77, A:N.102, A:N.102, A:D.103, A:S.129, A:S.129, A:T.130, A:G.131, A:H.152 Salt bridges: A:H.155 BMX.5: 20 residues within 4Å: Chain B: G.9, G.10, T.62, G.63, A.72, L.73, N.74, N.77, N.102, D.103, A.104, S.129, T.130, G.131, V.132, G.133, H.152, H.155, E.174 Ligands: ADP.4 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:A.72 Hydrogen bonds: B:G.10, B:T.62, B:T.62, B:G.63, B:N.74, B:N.77, B:N.102, B:N.102, B:D.103, B:S.129, B:S.129, B:T.130, B:T.130, B:G.131, B:H.152 Salt bridges: B:H.155

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: H.155, C.165, C.167, C.172 Chain B: Y.263 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.155, A:C.165, A:C.167, A:C.172 ZN.6: 5 residues within 4Å: Chain A: Y.263 Chain B: H.155, C.165, C.167, C.172 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.155, B:C.165, B:C.167, B:C.172

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thanuja, G. et al., Structure and Function of N‐Acetylmannosamine Kinases from Pathogenic Bacteria. Acs Omega (2020)

Release Date

2020-02-05

Peptides

N-acetylmannosamine kinase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

N-acetylmannosamine kinase